For desktop apps Flatpak is almost certainly a better option than Docker. Flatpak uses the same core concepts as Docker but Flatpak is more suited for distributing graphical apps.

1. Built in support for sharing graphics drivers, display server connections, fonts and themes.
2. Most Flatpaks use common base images. Not only will this save disk space if you have lots of, for example GNOME, applications as they will share the same base but it also means that you can ship security updates for common libraries separately from application updates. (Although locked insecure libraries is still a problem in general, it is just improved over the docker case.)
3. Better desktop integration via the use of "portals" that allow requesting specific things (screenshot, open file, save file, ...) without full access to the user's system.
4. Configuration UIs that are optimized for the desktop usecase. Graphically tools for install, uninstall, manage permissions, ...

Generally I would still default to my distro's packages where possible, but if they are unsuitable for whatever reason (not available, too old, ...) then a Flatpak is a great option.