In a vacuum, your suggestion would be kind of cool if well done. Seeing all the slight differences of a similar world where important NPCs are genderswapped?!?!! Unfortunately, one of the following ~has to be true.
1.) The swapped (I assume you want both sex and gender to be changed) characters act exactly the same, except for in sex scenes.
2.) The swapped characters act different, reflecting cascading differences that come from growing up as a different sex. Societal roles, norms, and all that. E.g., Minthara is now a male Drow who grew up in a matriarchal society, and thus would have a different personality/goals/outlook.

If #1 is true...we're treading perilously close to a change made *solely* for sex scene viewing changes. I suppose also romance, but you already have the choice to romance NPCs regardless of Tav's gender/race/sex. Larian now would have to animate twice the # of sex scenes to account for both versions of each NPC. Additionally, this minimal-effort change risks making some NPC's personalities/backstories inconsistent, if there's any gender-dependent aspect to those. And finally, trans persons are a minority that face injustice and real harm from society, so including gender options is an attempt to normalize their existence. The same can't really be said for the reasoning behind genderswapping NPCs.

If #2 is true, then that would require a TON of work, enough that it's probably not worth it. Also, the developer would be treading perilously close using gender-stereotypes and making statements on various gender expectations/societal roles.

tl;dr:
- If minimal effort is put in by Larian, it could introduce inconsistencies in NPC backstories/personalities, would still require work to animate additional sex scenes, and would be less real-world beneficial/inclusive than adding PC gender options.
- If a lot of effort is put in...obviously it'd take away from other things in the game.