Multiple lessons there for the defendant, not the least of which is don't do the crime if you can't do the time...the other significant lesson is don't be an aggressive individual after you have slipped through the administrative cracks.
As I read the article, I saw nothing that suggests medically-managed HRT, surgery of any type or even a legal name change...in other words, no overt steps to even suggest a rational basis for deviating from what most agencies do for housing (and I say most only because I am sure somewhere in the States someone likely would house the pre-/non-op in a segregated cell on the women's side of a facility out of fear of resource-hogging litigation).
