I don't think it's only uncomfortable for the reason it's supposed to be uncomfortable. Joanne's endings are weirdly and specifically transphobic. I hadn't originally wanted to see the ending in which Joanne was confined to the asylum but for completeness I did so and was surprised to find it was also transphobic for really no good reason.
Within a very short time-frame, in a very small number of words in Joanne's endings we see her deadnamed, erroneous references to "mutilation" and outmoded references to transvesticism. If it's all coincedence it's still weird to see so much hit so fast.
In the "good" ending she's left in the care of Sable and Amadronia but from the "bad" endings we can see neither one of them respects her, has her best interests at heart or cares about her well-being. On its own that's a really interesting story hook but in context of the weirdly specific transphobic allegory it's awkward to say the least.