If Non Binary Genders are Real and Just as Valid as Man and Woman...

[I spent the winter writing songs about getting better]

I've never really thought about this issue much...but honestly now that I have I can't say I'm quite comfortable with putting trans people in prisons of their preferred gender. Imagine what would likely happen to someone with a vagina in a men's prison, that could end up being a de facto death sentence, or de facto driving to suicide after regular rapes. Or conversely the obvious issue with someone with a penis in a women's prison, as insanely stupid as the conservative handwringing over bathrooms goes this is a bit different because, well one it's a prison, the most rape-filled places on the planet and two we're talking about people who are by definition already criminals. If we're talking about non-violent offenders or someone who can't "use it" due to hormone treatments it's a bit different situation granted but a mishandling of this could be catastrophic.

The only real solution is probably keeping all trans people in some sort of separated unit. If it's a white collar type prison with minimal security issues then general population might be OK. And yes, I'm aware of the torturous conditions Manning was imprisoned in and that's not OK, I'm not even someone who believes Manning should've received a prison sentence at all. But ignoring that some sort of alternate solution should probably be sought between simply "throw them in gen pop of their birth gender" and "throw them in gen pop of their preferred gender".

[I spent the winter writing songs about getting better]

Also I like how the OP doesn't even consider degendering prisons.

Locking women prisoners up with male rapists, sexual abusers and all sorts of violent offenders? I don't see a problem at all!