Can't that just be solved with this?

   alias foo="flatpak run org.blub.foo"

I would bet flatpak doesn't do this by default since it doesn't hijack a native package's namespace in the way Canonical is forcing people with snap hijacking apt install, and gives you a choice.

This lets me run multiple different Chromium flatpaks alongside the native package (stock Debian apt Chromium, official Chromium flatpak, Ungoogled Chromium flatpak) without issue, for example.