Let me guess, the only thing that seemed off to you about the king of Sparta deriding the Athenians as "boy-lovers" in
300 was the insinuation that homosexuality existed at all in ancient Greece, too, right?
I don't have time to go into the entire well-documented existence of what we would today call trans and non-binary people throughout history and across cultures, but here,
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And the other part is, no, this game isn't in "the past". It's in a fantasy setting already chock-full of anachronisms as compared to its primary real-world inspiration of medieval Europe. The creators can put whatever they like and it won't be out of place, because
they're who gets to decide what's out of place in a world
they made up.
And I point all this out as someone who isn't even particularly interested in trans content - the punk girlfriend is cis on my Summertime Saga save - I'm just not bothered by the mere acknowledgement that trans people exist as you seem to be by describing the modern world as "fucked up" for doing so.