The thing with appimages is that they expect the developer to have full knowledge of what libraries need to be bundled with their app, which makes it difficult to make truly universal appimages. In flatpak you just select one of a set list of runtimes and add any additional dependencies on top of it. Flatpak also re-uses the files for each runtime in between the different apps that use it, which saves a lot of disk space.
If you’re interested in another approach to containerizing GUI applications, also checkout out x11docker. It’s a small independent project maintained by one guy, nothing big like flatpak, but also pretty cool. The name is actually a bit limiting – it supports both docker and podman, and can run wayland apps as well. One of the coolest features, in my opinion, is the ability to run a separate X server inside every sandbox and forward individual windows to the “host” X server. That way you can prevent apps from spying on your keyboard or other apps’ windows.