Well put! I'd been mulling over this suggestion trying to work out why it made me uneasy, but you've now saved me the effort.
I think you're spot on.
EDIT:
I wouldn't rule out all possible NPC gender swapping. For example I wondered in another thread if a way to introduce romances with trans characters might be to have a character who was cis in some possible worlds and trans in others, but I don't think that's something that should be done in BG3 or rushed into, and if done at all should be done extremely carefully if at all for the reason you give. There is more to gender identity than appearance and a few additional lines, particularly for a character that comes from a society where gender matters.
Though changing the gender of a character can absolutely work in some circumstances with the right performances - look at m/Shep and femShep. And because in Faerun in general doesn’t have the same sort of structural factors related to gender that could give people outlooks based on that, it may not be a huge issue for most of the existing romances other than Minthara.
But still ... probably best avoided unless designed into the game from the start with a specific purpose in mind.
