Probably partly due to transphobia, but probably also partly because when one is arguing for a change (e.g. self-declaration of status), a natural focus is on who may be harmed by the change, and probably also partly because rather than thoughtful dialog being the norm, cries of transphobia are the norm, without addressing the concerns (including the concern that some cis male prisoners will try to exploit anything put in place).

The entire dialog seems extremely unhealthy, which ultimately I think hurts trans people more than anyone because usually they're least well served by the status quo, and progress is usually slower when dialog is unproductive (though that depends on whether dialog is necessary to achieve a large enough coalition to enact change).

One advantage of coming at it from a completely different angle--overhauling prisons, for instance--is that there is some hope of bypassing the dysfunctional dialog and getting something that would benefit everyone.