I don't think its transphobic but there is only so much you can do with a metaphor. To be truly diverse you actually have to touch upon a real issue.
Like the x-men works best when it using the mutant metaphor to reflect a real issue. For example Surge is a feminist but doesnt approve of Dust wearing a burqa and sees it as oppressive.
So in this case regeneration bypasses alot of the medical issues transgender people face so you have think of other ways to touch upon the transgender expierence.