I think that the book itself, rather than the film depictions, could resonate uncomfortably if through a lens of undergoing surgery/identifying as another gender.
How can I describe my emotions at this catastrophe, or how delineate the wretch whom with such infinite pains and care I had endeavoured to form? His limbs were in proportion, and I had selected his features as beautiful. Beautiful! Great God!
And there is the consideration that a woman who had experienced a premature birth and death of that child could have flipped those memories into a man performing a female role - bringing life but also experiencing a visceral revulsion at the result - is changing sex and gender based functions, roles and expectations in the text in a way that challenges beliefs that it's all fine to do that, it's never going to go wrong, as it very much isn't all fine. Adam feeling rage at what he is and seeking to punish the parent who rejects him is also going to hit the target with that person - that love/hate, wanting to be accepted but isn't, yes, that's going to speak to them. And, of course, the doctor believing he could do it and it would be perfect, then his rejection making him the monster - that's going to be difficult, as 'does the surgeon promising me this really think I'm going to be beautiful? Or does he think I'm a hideous creature he's experimented with?'.
So many ways this can be read quite reasonably from a pro-trans viewpoint.
I do not believe that makes it transphobic, but making somebody uncomfortable because it challenges their own beliefs - yeah, this person has a valid point that could have been discussed.
Proves that Mary Shelley was a fucking amazing writer, though, creating something where her ideas can be discussed in relation to something like this, doesn't it?