Meanwhile, you can have the best of both worlds using Nix. Tons of things are packaged already, and for the most part dependences are shared across many different packages. But if a package needs a special version of a dependency, thats no big deal.
This seems like the killer feature of flatpak.
Regardless, do you not trust the applications that you run natively?
Sandboxing has uses other than running actively hostile apps (for which I'd argue this kind of sandboxing isn't enough).