It'd be better and more comfortable to make task/workspace isolation easier. You have all your apps installed system wide as usual, and you isolate processes in sandbox per your current task.
Isolating individual apps and having to deal with permission prompts and protals, and persistence of permissions is uh, not very user friendly anyway.
Feels like this whole flatpak and similar mechanisms is more oriented on bringing in untrusted apps, rather than anything actually comfortable and useful as far as "work" isolation needs go.