Yes, but there's a big difference between a well-done trans NPC (especially a minor one) and a trans party member. I think letting non-cis people be heroes in such a mainstream title would have been an amazing thing for trans representation. If you wanted to avoid the 'trans is based on bits' potential issue you'd lock them coming out behind a high-approval probably Act 3 dialogue.
Hell most of the party are elves and despite it being canon that D&D elves are more commonly intersex and some are even sexfluid they're STILL all 100% cis.
Thankfully the modding community does what Larian doesn't and has added top surgery scars to Gale.