Libadwaita is only compatible with gnome and only works with gnome. Other DE's can try to make it work in their DE, but the experience for them is hostile.
Not sure what you mean with "compatible", as libadwaita apps are supposed to work on other DEs as well. It might not fit visually with them, but that's not being incompatible.
How about when the theming is baked in and impossible to change?
It can still be changed, it's just a harder to do so.
It's about doing things that go against the interests of the user.
This conveniently ignores that app developers are also users of ui frameworks, and they would like a well defined platform to test for, rather than an endless stream of distros each with its own theme that could break their app.
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.
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