I don't understand why you would start reactively uninstalling apps or control would be taken away, I don't believe any of them have gone closed source. If the app is open source then no control can be taken away from you, you can just grab the source and inject your CSS. Again would be happy to walk you through this process, but that would be in the worst case scenario, right now and for the foreseeable future it's unnecessary as you can still use the method I previously described with setting your user theme.
It also doesn't really make sense to me to uninstall some app because of some theoretical bad thing that could happen in the future, if you take that view then you would have to uninstall everything it seems, because there is always a possibility that developers make some decision you don't like 10 years from now when the computing landscape has changed. You can of course stay on an old version if there are some changes you don't like, the developers might grumble more and tell you to upgrade for usability and security reasons, but that's a decision you make according to your own risk factors.
>Flatpak
Huh? Flatpak is an API and CLI, it doesn't use GTK. The ways it's usually accessed through a GUI are GNOME Software and KDE Discover, but you don't have to use those.