I strongly agree; if you deprive someone of their liberty, then you take on the responsibility of protecting them - because you've deprived them of the ability to protect themselves.
I'm not aware of any prison regime that takes the safety of prisoners as a key objective. [Edit] Nor do I know of a state that handles the deliberate negligence of prisoner welfare as a criminal offence.
The data really really doesn't support your view. Men are objectively more dangerous.
https://www.statista.com/statistics/251886/murder-offenders-...
https://stoprape.humboldt.edu/statistics
An estimated 91% of victims of rape & sexual assault are female and 9% male. Nearly 99% of perpetrators are male
Perfect is the enemy of good and while it's hard to disagree with the sentiment of "reform that makes prisons safer for everyone ", we have no idea what that actually entails and that's so much of a monumental task that it's basically a non-starter. I feel like the sentiment here is "this wouldn't be a problem if we changed everything, so why don't we?"
I think people in prison should be protected from other people in prison if they are dangerous, and I think prisons fail to do that today. I don't accept your presumption that having a penis makes someone inherently more dangerous.
Again: if your goal is to protect women in prison, the best way to do that is to advocate for reform that makes prisons safer for everyone. Not by being transphobic, which you're doing instead.