For example, this is exported .desktop file visible from host: $ grep Exec ~/.local/share/flatpak/exports/share/applications/org.kde.discover.desktop Exec=/app/bin/flatpak run --branch=master --arch=x86_64 --command=plasma-discover --file-forwarding org.kde.discover @@ %F @@ Exec=/app/bin/flatpak run --branch=master --arch=x86_64 --command=plasma-discover org.kde.discover --mode update , but there is no "/app/bin/flatpak" file on host. It's "/usr/bin/flatpak" instead. One workaround here is to create "/app/bin/flatpak" symlink on host. I wonder if any better solution possible.
Is this with the Flatpak-packaged version of Discover?
Yes, but it occurs even without Discover itself, when installing from within it's sandbox command line.
I'm not sure this is really fixable from Discover. It's not discover who writes these files.
Indeed, this is not really fixable in any KDE code and arguably it's up to you to handle when you go poking about in the implementation.