Same prefer, although I'm not sure what you mean by "installing changes data in places on my disk"?

Nothing should change, all installations and addons go to the ~/.var directory. When you launch the application, yes it can start reading and writing to arbitrary places on disk, which is why I make it a habit of first launching Flatseal to modify permissions and know exactly what it can and can't do and reach.

I actually vastly prefer this methodology with what we have right now, but if it or something else adopted an application/directory methodology as you described I'd be elated.