I understand what you're saying, but I'm not sure if I agree. I think of what Ira Steven Behr said about the portrayal of LGBT issues on DS9, he really feels they missed the mark because they went with a 'technicality', because Jadzia was married to a woman while in a male host, and those thoughts and feelings carried over, and he didn't feel it was actually a portrayal of a lesbian romance, but a cop-out.
There are other episodes which, while groundbreaking at the time, clearly used their allegory to soften the message somewhat. Frakes has lamented that Soren in "The Outcast" was played by a female actor, for instance. Using a female made the relationship more acceptable to the viewer.
I will say, however, that in Enterprise's "Stigma", which on the AIDS crisis via Pa'nar Syndrome, the allegory does allow them to hold up a mirror to intolerance and prejudice. Maybe that's what you're getting at? By showing the relationships and nonbinary gender identities as normal, rather than couching them in a metaphor so they could show the ugliness of intolerance, the writing doesn't go far enough?
It's an interesting point. My instinct is that we're mature enough to see things like gay relationships now without needing to obfuscate them in metaphor, even if the point is to highlight the flaws of intolerant views.
Why make up a religion, when you can join an already established one, and then foment a schism? The Church of the SubGenius welcomes all heretics.