For 2, there are ways to install packages without messing with the read only file system. Easiest ways are using nix packages or using distrobox to install non-flatpak software.

So for the linked aur PWA package you provided, you could create an arch linux distrobox, enter it, install yay (or another aur helper), install firefox and your pwa package, and then use the distrobox-export --app <package> command to make the installed software directly runnable from the desktop.