Flatpack and Appimage formats do not provide the kind of process and filesystem isolation that Docker does. I would not be comfortable running run a service like Cloudron if it allowed running things other than well-defined/managed containers.

Yes, there are ways to break isolation and escalate out of a Docker container, but flatpack apps can, essentially, write anywhere on my system. Updating the ecosystem is also much more difficult; by comparison, it is possible to auto-build Docker containers from source and track recent updates/manage timely security vulns in a way that flatpack/appimage packages do not/rarely do.