This is where I’m at too. If I go crazy and start installing stuff natively to experiment I end up with extra stuff auto configured that’s no longer needed and random problems I’m too lazy to figure out how to solve. Flatpak doesn’t do that and I don’t have to worry about that. I can install random stuff to play with and uninstall it cleanly. Some packages need more system access than flatpak gives natively and with those I’ll make the decision of if I want to set it up and tear it down manually or not.

Storage is cheap, my time not so much.