Is the a downside to repacking the deb package? They’re basically just zip files of the same binary you’d run on most other Linux distros.
Reposting the link from another comment on here, there is a PR to build the flatpak from source https://github.com/flathub/com.bitwarden.desktop/pull/222
Why on Flathub it says that it “uses legacy windowing system”, but there is granted permission to use Wayland socket in manifest?
No, its certainly not because of that.
Many apps have both permissions simultaneously and theres no warning. In this case X11 is used as a fallback if wayland is not used.