Hmm, I'm not familiar with the cases but in particular the lawyers defense thing seems like it might be an overly simplified ragebait summary. For a start trans women can have penises but also, if said person no longer has one but raped someone when they did, it not being there anymore isn't relevant to the action. It'd be like if you punched someone and they fell and hit their head on the curb and died, but in between that incident and the trial you had the hand amputated, it wouldn't change what happened. I might have got the wrong end of the stick technicality wise but if that defense stood up that's a problem with the lawyer and the system.
As for the prison service not being suitable, a lot of nonces / abusers of either sex get done in whilst serving time, pedophiles aren't let off because prison might not be safe / suitable for them. So again if something like that has happened it's a problem with the system for sure.
Absolutely agree with what's in bold, but as the rest of my post suggests, I remain unconvinced of the notion that people are getting let off relatively scott free of punishment for serious crimes because they're transgendered. Obviously if what you've said is exactly how it went down then it makes no sense, it's hard to see both how and why that would be the case, but to my mind just seems a bit culture war esque.