In the upstream report, upstream confirms that gnome-shell itself does not need 'gjs', only the gjs library.
The gnome-shell-extension-prefs app packaged as a .deb correctly depends on gjs.
A default Ubuntu Desktop install includes gjs. For you to remove gjs, you will have needed to remove the GNOME Characters app and the Desktop Icons NG extension and the ubuntu-desktop metapackage. At that point, you're outside the fully supported Ubuntu Desktop experience.
Maybe the Flatpak needs to bundle 'gjs' if it requires gjs.
I am closing this bug.
In the upstream report, upstream confirms that gnome-shell itself does not need 'gjs', only the gjs library.
The gnome-shell- extension- prefs app packaged as a .deb correctly depends on gjs.
A default Ubuntu Desktop install includes gjs. For you to remove gjs, you will have needed to remove the GNOME Characters app and the Desktop Icons NG extension and the ubuntu-desktop metapackage. At that point, you're outside the fully supported Ubuntu Desktop experience.
Maybe the Flatpak needs to bundle 'gjs' if it requires gjs.