It looks like that problem is fixed with Flatpak override and not installing the Flatpak with root?
This is also probably because the Signal Flatpak is community developed on Flathub from Signal's .deb, they're not building Signal with Flatpak in mind. Mozilla provides an official Flatpak release of Firefox.
I'm sure official Flatpaks do better on average, but that narrows the selection a lot. And most third-party packagers raise my suspicions in a way that, say, the Debian packaging team does not. You should see my eyebrows go up when I cruise dockerhub!
I don't know what the right answer here is, but for me it's not Flatpaks or Snaps. Trusting the packager (and the org behind the package system) is a huge part of it. I breathe a sigh of relief every time I see the software I need is in Debian's repos, even if that means they may not be optimally sandboxed.
FWIW, PhotoStructure has an AppImage edition and it can upgrade automatically in-place.
(There's also a docker image, a macOS DMG, a Windows installer, and other editions as well--and yes, you can configure any edition to _not_ upgrade automatically if you prefer).
It _should_ work just fine. I have several Fedora users (because they emailed me, not because of any analytics: nothing "phones home" with usage, but I do use Sentry for error reporting, and that can be disabled).
If you see any errors, please email me (support@photostructure), post to the forum, or ping me on discord (links to those are in the footer of every page on photostructure.com).
My installs of Signal and Firefox are with Flatpaks and GNOME Software transparently handles updating both.