of course I've seen people argue on twitter claiming Yu can't be trans ANYWAY, because "biology," which at this point is less misunderstanding the text and more just arguing with the author over her understanding of transness. IMO the fact that Yu "was always a woman" but "assigned male by her mother" is a very deliberate point Inori's making about the validity of trans women's womanhood: to deny Yu is a woman is to deny the factual reality about her, rather than making any sort of subjective or "political" claim. The same is true about non-magical trans girls IRL. If a woman tells you she's a woman then she's a woman, period, regardless of how you might have interpreted her before.
Unless they're complete idiots, which can't be ruled out either, twitter being what it is, it's more likely that they're not denying her womanhood but rather only seeing her being born as a woman and now living as a woman again. Only looking at the very beginning and end of her story it's easy to think of her as having not changed at all. But she certainly has very much gone through what essentially amounts to the trans experience, having had to live most of her life as a man.