I know you like "logic," so you should know that one statement does not causally follow from the other nor are they making the same argument. If I wanted to argue "allow whatever the player wants," then I would have written that, but I didn't. I asked a question about the GM's power to change the world to accomodate the player and how the GM's world would somehow break if they were included.
Okay, which is fine, but we should both recognize that creating a space for playable yuan-ti in your world doesn't necessarily turn your game into a kitchen sink world. There are plenty of other ancestries that are probably off the table, and with a limited number of players, it's likely that players won't ask for everything. Moreover, a kitchen sink party doesn't necessarily mean a kitchen sink world.
Cool. So this is what you should start with telling the player, though hopefully doing so respectfully with compassion and a willingness to listen to the players' desires. If you talk with the player then maybe there is a more appropriate ancestry that does fit with your established lore. But simply saying "No!" upon hearing the request IMHO does more to fuel problems at the table than it solves.
Would you make me aware of those restrictions when you pitched the game to me? Or is this something that I would find out after you invited me to your game and I'm already at your table?