I agree with the criticism you've received, personally.
The fact that you as an author are using these pronouns for the character when communicating to me, does feel indicative of a larger problem. You describe this character as being "in denial" yet still seem to want to say that the character identifies as a boy. These are two somewhat different ways of relating to a past. There are many trans people who will say things like, "when I was a boy" etc, but generally they do not necessarily see those periods as being in denial, so much as a genuine identification with that gender at the time. Many people also have fluid identities, or may be a trans woman who just happens to like the way he/him sounds, or maybe just doesn't care about pronouns. But the way that you are going about this doesn't really read to me like it's aligning with an intention to understand and represent an authentic trans experience. You are an author with the omniscient level of understanding of your story and characters, and it feels gross to not use that to respect a trans character's identity as you know it. It seems weird that you would want to rep this like self-discovery of an identity that was felt the whole time, but still want to rep this like a fluidity approach where you're referring to the character as though you yourself are another character in this story. Also, the egg experience sometimes includes signs. Sometimes it doesn't, but sometimes it does.
If it is your specific trans experience, as an openly trans author, to experience this simultaneous fluidity and also having identified a given way all along without realizing it, that is a different matter. You'd be writing from your own experience, and the readers would know that you were being authentic and not just looking for an excuse to misgender a character.
When writing about trans characters before they are out, you need to understand and respect your trans audience members, and the way you write your trans characters will be something that some people will go back and re-read and maybe have to process their feelings about.
What might writing this (a character coming out partway through a story) look like? Maybe it's having the story written in the distant past, or through flashbacks. What kind of narration are you using? Third person? Whose point of view? Is this a major character, or a minor character mentioned a couple times? Is there a way to make information clear to the audience and utilize dramatic irony?
Also, WHY does this need to be framed as a surprise or plot twist? What indicators are you having of the character being in egg mode (if applicable)? How are you handling this character with care and seeking to represent trans people as we feel represented by?
I Wish You All The Best by Mason Deaver did a great job of showing the first scene as being the point where a traumatic coming out had already happened, and the audience read what happened in the coming chapters. This is also a great way to frame coming out to the audience.
Think about it this way: if someone puts down your book and talks about the character, they need to be gendered correctly by that audience. You as an author are already being really weird about that. (I'm open to other trans followers feeling differently about this and sharing their thoughts in the replies/reblogs.)
Just personally, I feel really weird about the way you're writing this and talking about this and I think you're punching above your weight class in terms of trying to represent this specific kind of trans experience. I would either just not do it this way, or heavily change what you're doing.
The books of Tess of the Road by Rachel Hartman (I believe In The Serpent's Wake had this part) include a character called Spira, who is intersex and who uses they/them until the end of one of the books where Spira is offered the chance to try on other pronouns, where Spira opts to try on she/her as an experiment. The POV (from what I can recall) was third person limited, with a bit of a revolving point of view, and this scene is told through a different character's point of view. The narration changes at this point, but I feel like that's done really well because it's seen as just kind of a surface level trying-on-as-an-experiment thing, and that they/them were also very much accurate pronouns, and she/her isn't necessarily representative of womanhood, so much as pronouns themselves.
Honestly I may need to percolate on this one a bit more, but these are all my initial impressions of your approach as a trans person.