> 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
The Linux kernel allows you to run proprietary apps because the kernel code and the userland code exist in two separate "planes" connected by the syscall interface. The kernel even has an explicit exception for any code that may need to be shared between the kernel and the userland to make clear that this code is excluded from GPL.
As another similar case, the Free Pascal compiler is licensed under GPL including the runtime and almost all libraries/units that come with it but it also has an exception to allow linking without having the GPL extend to the programs the users write. AFAIK the GNU C library also has a similar GPL-with-linking-exception license.