It's not true they assume full write access to ~, they just don't propagate they limitation of a constricted choise of paths in their GUIs. Because they isn't a way to do that, GUI toolkits don't really provide a way to clearly communicate you can only save/open in a specific dir.
Flatpak aware apps (like the ones I develop, or any on elementary OS since flatpak is the native packaging format there) tend to just work.