Yes, I’m running a single theme instance and I’d like to keep it that way. It’s much simpler for the users.
I’d be happy with some hacky solution, like being able to inject custom CSS/JS based on the color scheme.
But ideally, each color scheme should have an option—in my opinion—to determine whether it picks up the dark or the light logo. Deciding automatically based on the base background color doesn’t work, exactly because the header background could be completely different.