For starters, I don't think Ron would have bonded with her on the train as easily as he did. Young Ron is honestly pretty uncomfortable/awkward around girls... unless he's able to put them into a category like "little sister" (which doesn't count.) Or "Hermione" (which doesn't count.) It's kind of a plot point in Book 4 that it takes him a while to realize she's a girl he could potentially ask to the dance.
The only way Ron is bonding with Harry on the train is if Harry is a HUGE tomboy... which I don't think is the case, because Petunia is dressing Harry at that point, and would be dressing her pretty femme (because Petunia is so strict Gender Binary herself. Instead of wearing Dudley's old clothes, Harry's probably wearing Petunia's old clothes.) I really don't think Harry would have been treated better/all that much differently at the Dursley's if she were a girl. Maybe less physical bullying from Dudley... but Dudley honestly doesn't manage much physical bullying as it is, because Harry is so much faster than he is.
If anything, Girl!Harry would have just reminded Petunia even MORE of Lily, and stirred up even MORE complicated emotions. And we'd get even more of live in chef/maid Cinderella!Harry. It would all feel very Matilda.
I actually think that Harry would be at kind of loose ends on the Hogwarts express, and get sucked into the search for Trevor the toad as something to do, so she would end up bonding with Neville. Hermione would be there too but well - Hermione rubbed Harry the wrong way at first in canon, and it would be even more the case here. They're both (functionally) muggleborn girls - but Hermione is SO much better prepared, and has SUCH loving parents, and won't shut up about any of this. In a way that Canon!Harry kind of fixates on Draco for ending up with his Ideal Life, it's possible that Girl!Harry might fixate more on Hermione.
11-year-old Draco would have treated Girl!Harry exactly the same, meeting her at Madame Malkin's and later on the train. He'd still have his obsession with her, and yeah, it probably does read as more of a crush to his Slytherin buddies... but I really do not see that stopping him. If his father can't get him to be normal to Harry, then that's just how it's going to be. Harry still gets Sorted into Gryffindor. But I don't see her getting close with the other Gryffindor girls: Lavender and Parvati just have very different personalities. And Harry and Hermione... are both very intense people who work best when they're able to take breaks from each other. In Book 4 when Harry is exclusively hanging out with Hermione, he comments that she's not as *fun* as Ron. And we see that dynamic again in Book 7 when it's just the two of them in the tent. Like they're incredibly effective, but seem to be wearing each other down a little. I think that forcing young (less emotionally mature) Harry and Hermione to be roommates would just end up with them getting on each other's nerves.
Hermione might get pulled into the friend group when Harry and Neville need help researching Nicholas Flamel, but she could easily stay more of a supporting character or even a frenemy in this version. Girl!Harry would still be the youngest seeker in a century. (Draco would be even more motivated to steal Neville's Remembrall if Neville was Harry's best friend... so that face-off would have gone down exactly the same.) Once Harry is actually on the team, I could see her falling in more with the upperclassmen, and hanging out with Fred, George, Lee, and Angelina (especially if they put together that she's a bit lonely.) It could be Harry, Neville, maybe Hermione, maybe the twins solving the puzzles at the end of Book 1. They'd still suspect Snape, who... would honestly be just a slightly different flavor of antagonistic and weird to Harry, if she were a girl.
Second year, Ginny would be Sorted into Gryffindor and I do think that Girl!Harry and Ginny would get along great, absolutely be bros, especially if they bond over quidditch and Harry can get more of a sense of Ginny's actual personality. I have to think 11-year-old Ginny would be much less awkward around Harry if she were a girl.
Which would be really intense actually, because Ginny would have shown up to school with the the Diary, and it's... sort of important to the plot that she's isolated and has no friends. If she shared it with Harry as a cool thing to look at - Harry would ABSOLUTELY get obsessed with it.
And since Harry's a much better *get* for Tom (Tom talks about being *so* pleased when powerful, important, future nemesis Harry starts writing to him instead of Ginny...) I think you just get Possessed!Harry opening up the Chamber of Secrets. Also, would Harry have a crush on Tom? We know that Canon!Harry thinks he's very handsome, and Tom Riddle can absolutely turn on the charm when he wants to, and might be inclined to play it slightly differently for a girl. He'd work VERY hard to to get Harry to distrust her friends. Really, you'd just get Harry's plot about being isolated and possessed by Voldemort in Book 5 being moved to Book 2. Tom would get Harry to write "her skeleton will lie in the Chamber forever" on the wall, and lure her down to the Chamber of Secrets.
However. I do think that Lily's magic would make it impossible for Tom to actually drain Harry's life, although he would try. It's be like the moment at the end of Book 5 where Voldemort tries to possess Harry, and Harry fights him off. So... I think Harry just wakes up in the Chamber with a basilisk she can control, since of course she's still a parseltongue.
The question is... what happens to the Diary, now that Harry knows it's dangerous? I'm thinking that when Harry disappears, Ginny freaks out and tells one of her older brothers, who tells Arthur, who tells Dumbledore. Dumbledore now has Harry and a Horcrux that still works... and it seems like if you've got school-age Tom Riddle right there, that would be a much easier way to get an answer to the question 'how many horcuxes did he plan on making?' So he'd get a head start on that project.
Harry now effectively is the Heir of Slytherin. She can go to the Chamber whenever she wants, and the basilisk is just her familiar I guess, which is cool. I could see a Harry who gets more *interested* in Salazar Slytherin after this. I don't think this helps her relationship with Draco any, who would literally die of envy if he ever found out that Harry Potter was hanging out in the secret Slytherin Chamber, able to control a millennia-old snake. But Harry might try to pick like, Theo's brain or something.
I don't see all that much about Book 3 changing until the climax - because the crew Harry takes down to Hagrid's after dark *would* be different. Neville, Ginny (not the Twins - I think they give Harry the Map and peace out, they've got their own things going on in the background and don't want to hang out with their much younger sister.) Maybe Theo? I could see him taking on a very Hermione-ish support role.
But that's also a problem, because if Ron isn't there, Scabbers isn't with him. And if Scabbers isn't with Ron - I don't think Remus notices Peter on the map, and so just stays inside and drinks his Wolfsbane, which means Snape doesn't go down. And since Sirius' target was never *actually* Harry... I think this is just a universe where Sirius first-degree-murders Peter, and doesn't have a confrontation with Harry at all.
I do think Voldemort still comes back though. Trelawney would still have made her prophecy ("His servant has been chained these twelve years. Tonight, before midnight... the servant will break free and set out to rejoin his master.") But in this universe the prophecy would refer to Barty jr, finally starting to throw off the Imperius curse. Which we know he does do, at around this time.
Bertha Jorkins still goes on her trip to Albania, and I think... Voldemort just possesses her the way he did Quirrell. It's probably easy to do after someone's been sort of fried by a memory wipe. Also, being in her head, I have to assume he's going to eventually gets some inkling of the fact that Barty is still alive, and so goes looking for him. Harry is still at the Quidditch World Cup because she's friends with Ginny, her scar is still hurting (she probably writes to Lupin about this, instead of Sirius, but Lupin gives her pretty similar advice. He will have still left Hogwarts, because Snape will have still outed him as a werewolf at the end of the year.)
Harry still ends up as Champion... although I'm thinking Big Sister Fleur would be a little more protective of Girl!Harry than Boy!Harry. Also... I think Harry just straight-up has a crush on handsome, nice, good at Quidditch Cedric. Rita could write about the Harry/Cedric/Cho love triangle, instead of the Harry/Hermione/Krum love triangle.
(Harry asks Cedric to the Yule Ball. It doesn't work. She goes with Neville as friends, and Harry/Neville miiiight be the endgame ship in this universe.)
I'm not sure Barty would be able to take care of Voldemort AND prep the ritual to bring him back to life AND impersonate Moody though. He needs a different man on the inside. I think at first he tries to use his father - but as we know that gets risky, because Barty Sr is remarkably good at fighting the Imperius curse, and also just knows way too much. He's a huge risk, because if he goes rouge, he'll tell Dumbledore everything (as very nearly happens.)
So I think Barty Jr. targets Barty Sr.'s assistant Percy Weasley instead, after he can no longer control his father. Uses him as a way to affect things in Hogwarts. He might imperius him, but he also might just like... Polyjuice himself into his father for short periods, and manipulate Percy in a non-magical way, to make sure he helps Harry, and gets her to the cup first. Once Percy realizes what he's done... I think he re-commits to his family in penance, and stops being a such a Ministry man.
Voldemort rising works as kind of a reset button, so things would start looking a lot more canon again after that, only with Ron and Hermione swapped out for Ginny and Neville. Main difference being, Voldemort has Barty now. I absolutely think he would have survived Book 4, and I actually don't know what the dynamic between him, Lucius, and Bellatrix would be. Probably pretty antagonistic, because I get the feeling Voldemort would have fun playing them off against each other.
So I'm going to leave this what-if here for now. Thanks for the ask, this was a lot of fun to think about.