Another solution to this situation is to squash your changes in place so that your branch is just 1 commit, and then do the rebase against your master branch or equivalent.
Works great if you’re willing to lose the commit history on your branch, which obviously isn’t always the case.
It looks like there are instructions here about hosting your own flatpak instance: https://docs.flatpak.org/en/latest/hosting-a-repository.html