I have quickly scanned the Flatpak documentation and found this info about bundled dependencies (Dependencies — Flatpak documentation):
As will be seen, bundled dependencies can be automatically
downloaded as part of the build process. It is also possible
to apply patches and perform other transformations.
Having bundled dependencies directly linked to the repositories used by the Slicer superbuild and the SystoleOS patches available in the SystoleOS/gentoo-overlay repository is one possibility. In the SystoleOS project we are trying to contribute all these patches to 3D Slicer, but some of them might take time and some others might not even be accepted.