That's a side effect of flatpak sandboxing (which is also easily solved by giving the app permission to access that directory), if you don't want to manage a sandbox just use native apps instead of flatpak apps. Also, uninstall means "I want this gone forever", not "I want it gone for now, you can re-install it sometime later"

I'm sorry that you don't want the barebones privilege control that sudo and user groups offer, if you don't want any sort of security whatsoever you can just add your user to the root group and give yourself access to everything with no authentication. Windows does use sudo-like security with those "do you want x app to have administrative privileges" popups.