While what you say is true, the “portals” were an afterthought, an imposition to developers and a cumbersome and poorly documented solution. Just like the theming and most other things.
Instead of bluntly blocking things why can’t Flatpak just simulate a full environment and just prompt the user whenever some application wants to read/write to file / unix socket at some path? A GUI capable of automatically enumerating those resources and a bunch of checkboxes like "app X and Y both have access to socket at /var/run/socketY would also solve most of the issues.