I'm trying to inform my reading of the end where Joanne gets stuck in Amadronia by what I've seen in the other endings so conflating them is certainly a risk. When I saw the ending in which Joanne stays in Amadronia under Sable's guidance it reads quite well. Joanne appears to be suffering an analogue of trauma induced body dysmorphia. With the information he has it's perfectly reasonable for Sable to assume this is in her best interests, even if Amadronia is far from an ideal environment there really isn't a suitable facility for her or any of the demihumans still locked in the asylum. The problems only arise when we see what Sable does when he realises what he wants and what Joanne wants are in conflict.
The idea that Sable is shocked and reacts poorly tracks very well with his character. He's a shut-in with a slightly problematic fixation on demi-humans. If the story hadn't stopped there I'd probably assume he would eventually learn his lesson and apologise. Since it does cut there the place where it cuts has additional significance and since it's a bad end it seems we're to assume the current situation is extremely bad. The current situation is Joanne is genuinely happy for the first time we've seen her, she's comfortable, she's stopped self-harming. The implication is that this is bad because Sable believes she should be forced to live as her birth species and he specifically uses transphobic language to dismiss her. Since he's the one unhappy with the current situation and this is a bad end it feels like we're supposed to agree with Sable here.
If that's a bad reading then the implications on the main ending are substantially different. Amadronia is still a terrible environment for Joanne, Sable is still hopelessly out of his depth. But if he is prepared to put her needs above his own after all then the ending is bittersweet rather than pure grimdark.