GNOME devs never said that theming is incompatible (just “not supported”), and you’re still not explaining whay you mean with “incompatible” either. Managing window controls also doesn’t seem a requirement to be “compatible”, as the app still runs fine even with client side decorations (again, it just won’t fit visually with the rest of the system).
And by the way, the problem is not theming per-se, but the fact that apps get themed by default, they inevitably break by default, and app developers are left to deal with that. Nobody ever tried to improve the situation so the solution they came up with is to have their apps always look the same.