The only reason Gosho would ever want Detective Conan and Magic Kaito to be separate universes is to cover up his own mistake in making them intertwined at all. And even then, it’s really just because he doesn’t want Akako magic in Conan’s world, not because he didn’t mean for them to cross over. Him backtracking because he realized an issue I do not take as an excuse to say they are separate universes. More likely he did want to write them as happening in the same universe, did write it like that, and only made up an excuse after he went too far with it. Aside from Akako, every relevant Magic Kaito character has appeared in Detective Conan (or mentioned, with Phantom Lady for Chikage), and Kaito is clearly still looking for one gem in particular. That story is clearly the same.
The issue I see with other people is for Detective Conan in Magic Kaito. ( Which overall is extremely unfair since the majority of MK came before too much involvement in DC, so saying that there isn’t as much evidence when you barely see any MK is a terrible argument. )
But, the chapters that do come after DC reference DC things too often to be written off. It’s easier to take them as actually attached to DC than try and say ‘everything is happening the same just not in the same universe’ for one ‘problematic’ character that doesn’t even show her face in the ‘logic’ side of the crossover and isn’t overt now anyway.
1) Shinichi outright appears in Magic Kaito. In a similar cameo to Kid’s heists in Detective Conan, he and Megure pop up and give Kid a bit of trouble. And this is all in flashback, prior to the Suzuki Black Star heist that marks their first meeting after Shinichi shrunk in DC. Shinichi never saw or really knew who he’d been up against (which I still find mildly odd, because sure it was never said over the radio, but people were down on the ground with signs, did none of those say Kid), him not realizing in DC could be kept.
2) Chaki (Nakamori’s boss) was introduced in Kid’s first DC appearance, and came over to MK during Nightmare’s chapters.
3) At the end of the Phantom Lady chapters, Kaito is clearly going to do the Ryoma heist in DC afterward.
4) Jirokichi was clearly given a reference at the beginning of the Corbeau chapters.
5) Any and all Kichiemon encounters from Kid have only ever been shown in Detective Conan. Eccentric Mansion, the Iron Tanuki safe, Kirin Horn heist. The Sun Halo incident reference it both in the fan popping up after possibly killing the people trying to get into the safe and Kaito’s reaction to it.
( ‘Oh great, now you’re in my story, too. Don’t think I didn’t recognize that. Why couldn’t you stick to popping up with the small detective? Kindly refrain from impaling my girlfriend, you maniac.’ )
Magic Kaito is written far too rarely to just dismiss every single reference and nod as ‘same thing happening but not in the same universe’. If the story basically directs you to the other series for continuation (look under point 3), it is crossover in the same universe. I don’t care if Gosho said things to try and cover his tracks after looking at Akako again, he dug his hole himself.
