Yes, Flatpak is overall a better approach when compared to AppImages, since being dependent on a known runtime ensures the program will run whenever the runtime is available.
What I wish they would add is a way to run the flatpak in a portable way. Because as it stands, AppImages is the only option for that. Flatpak doesn't really allow to have a portable installation in a pendrive, for example. At the moment there's no replacement for AppImage in such use cases, which is a pity.
But there's no fundamental technical design roadblock in flatpak that would prevent it from supporting this in the future, imho. theoretically one could create a program that mounts the flatpak file into a ramfs layered with the runtime and run it.
You are mixing different ideas of freedom. Software freedom is not the same as freedom of choice of software.
You don't need Linux to have choices of what software to use, you have that in most (all?) proprietary systems, in some you might even have more choices than in Linux.. even if it includes proprietary software.
This is analogous to how being a free person (not a slave) is not the same as having freedom to choose who to work for, even if some of them are slavers (ie. having freedom to choose your master).