The bundle concept applies more to AppImages than to Flatpak. Flatpak downloads common runtime libraries and packages and uses them to run all GUI packages in a sandboxed environment using bubblewrap. OStree is also involved.

I dislike Flatpak because it encourages package maintainer obsolescence. I heard a guy from OpenSUSE saying in a MicroOS presentation that why create, manage, and use RPMs when we can just use Flatpak. I also don't want to touch Flatpak anymore because people from GNOME are involved in it.