System runtimes considered unused even though they are used by user apps

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Linux distribution and version

Fedora 30

Flatpak version

flatpak-1.2.4-2.fc30.x86_64

Description of the problem

When --system runtimes are only used by --user apps, then Flatpak considers the runtimes unused.

Steps to reproduce

Install an application, it gets installed as --system by default:

$ flatpak install flathub org.gnome.Documents

At this point, realize you would have preferred to install it as --user, so uninstall and reinstall:

$ flatpak uninstall org.gnome.Documents
$ flatpak install --user flathub org.gnome.Documents

The app works just fine: Flatpak uses the system runtime even though the app is installed for the user.

However:

$ flatpak uninstall --unused


        ID                                Arch           Branch
 1.     org.gnome.Platform                x86_64         3.32
 2.     org.gnome.Platform.Locale         x86_64         3.32

Proceed with these changes to the Default system installation? [Y/n]: 

Proceeding would break the installed app, as it would find itself without a supporting runtime.

If Flatpak can run a --user app in a --system runtime, then it shouldn't consider the runtime unused.