I feel like you're conflating the Joanne ending with the rest of her route and forgetting that the characters don't have the same insight into her situation that you now do.
It's easy to complete the Joanne ending and say "ah, so that's what she wants" and to look back over the rest of her route with that insight. But the characters in the game don't have that leisure. They don't know that she wants to become human; only that she keeps harming and denigrating herself. They don't link her self-harm with her not feeling comfortable in her own body; they only see self-destructive behavior.
Take the other ending, for instance. She isn't being confined because she wants to become someone else, or to stop her from undergoing such a transformation. She's confined because she's repeatedly self-harmed, and has now started physically hurting the people around her.
As for the Joanne ending, I understand your concerns with Sable's reaction, but I think it speaks more to his shock than anything. He hasn't seen her in months, now she's suddenly lost her demi-human aspects and taken on a new name. His inability to immediately adapt to her new name and appearance is unfortunate, but I don't see it as transphobic.
If that ending lasted a bit longer, then he might have gotten used to calling her by her new name. After having a chance to sit down and talk with her about her transformation, he might be able to accept that this is what she wants, and that what he called mutilation is actually something far more positive for her. Of course, the game ends before they have such a chance, so all we see is his initial failure to cope with this sudden change.
Anyway, if you view Sable's reaction in the Joanne ending as transphobic, then I can at least understand why. But I don't see how you can apply that to the rest of her route or the other endings. Their desire is to stop their self-harming friend, who's been overworking herself, not sleeping or eating properly, and violently attacked someone, from spiraling out of control any further.