The question is, do they change the remote or just hide the apps?
I currently use 2 flathub remotes, the verified (named flathub-v) and the unfiltered one. When installing from CLI I can see if it is verified (2 possible remotes show up). I hope COSMIC store and KDE Discover will show the verification check soon.
But a few popular ones are not, like VLC (developers dont know Flatpak, should get an introduction by the current maintainer), Inkscape, Spotify, Steam, Bitwarden, Signal, Torbrowser launcher, Blender, Calibre, and more (excluding Chromium Browsers, use the native versions for security reasons) are all missing.
Important things to consider:
distro packages are nearly always unverified i.e. maintained by distro packagers instead of upstream
spotify flatpak is not verified, but the flatpak is securely packaged. Mint has a deb repo, and that proprietary piece of malware could do whatever they like with your entire system
flatpaks are very often more secure, at least they have some security mechanism that can be easily manually hardened. Unlike firejail or bubblejail, which are very complex.