> If your application links against the runtime, be it dynamically or statically, then it is a derivative work and thus must be distributed under the GPL

Flatpak apps aren't linked against a runtime, they just run in a bwrap sandbox with that runtime. Again, think of it as a Docker container.

In Fact, Flatpak apps aren't even supposed to know they're running in Flatpak. They can know that, because the user agent string says so, but nothing in the app code specifically should be adapted to run in Flatpak