Desktop entries ignore `FLATPAK_USER_DIR`
If the location of the Flatpak user installation has been customized via the FLATPAK_USER_DIR
environment variable, Flatpak apps installed to it will not appear in Overview search results.
It is still possible to use the flatpak
commandline utility to install, display, and run such apps.
An interesting case is that GNOME Software is able to install Flatpak apps to a customized user installation, but cannot run them; after a (successful) install of such an app, the button to launch it does not appear: