The rape occurred in 2004, when the rapist was living as a man.
There has been neither surgery nor, from the way I read the article, any hormone treatment. Yet there was a name change in 2012.
So still fully functioning biologically male anatomy, and a rape conviction. Yes, that should mean make prison. Child rapists are often placed in solitary anyhow, for their own protection. One more handled that way won't be an issue.
It would be completely different for someone convicted of a different offence, or if further along the medical transition pathway. After all, no-one would have put Hayley Cropper in a male prison, would they?