Confirmed that Firefox is indeeded Flatpaked by looking at the repo.
Flatpaks (at least for KDE) are @ bazzite/installer/kde_flatpaks/flatpaks at 85a1e0d275f5699416a61ad483aba649333de16d · ublue-os/bazzite · GitHub
And you can see system package being removed in the containerfile.
I’ll try and figure if people had any luck providing the system package in this thread: Can't layer firefox - #7 by SuperFunHappySlide