Yes, you're right. I agree it all seems very strange.
What we have is two ideological modes operating under the same brand.
One - the academic, queer theory mode - denies sense to talk of identity, stresses fluidity with something like Derrida's endless deferral of sense and tries to link this to Butler's egregious misreading of Austin's notion of the performative.
The other - out in the wild, so to speak, in schools, council meetings, political parties and so on - reifies gender identity in a wholly dualist manner, opposing it to bodily sex and taking a quasi religious stance to its mysteries.
Even if either of these modes could be made coherent in itself (I see no way of doing this), it's plain as a pikestaff they can't be joined in any coherent whole. But, well, there they are.
It would help a little if those in the academy on mode1 could offer the obvious critique of mode2 from their own standpoint. (Gender identity true believers cannot be expected to criticise Judith Butler etc., so the reverse cannot happen.) But those who started the whole thing (who they? - not allowed to say on MN) have too tight a grip.
Really, it does look as if the academy has been baldly pusillanimous on this. Easy for me to say, I know, now my employment does not depend on toeing the party line. But, really, you all need to stand up and be counted. I'm sure it will come; some people I know are already girding their loins. Go for it.