The problem of there being a separate runtime for each video driver version was explicitly discussed in the article:

If you are part of the huge part of the population who happens to own a Nvidia GPU, it's a whole other can of worms. There are Flatpak runtimes that target specific Nvidia driver versions, but they must be matched with a compatible version installed on the host system, and it is not always a process as smooth and painless as one would hope.

An improvement idea that is floating around is to, basically, just take a step back and load the host drivers directly into the runtime, rather than shipping a specific version of the userspace drivers along with the application. Technically, it is possible: Valve's Linux runtime is pretty similar to Flatpak architecturally, and they solved this problem from its inception by using a library called libcapsule to load the natively installed host drivers into the Steam Runtime. This is the reason why it's significantly rarer that an old Steam game fails to launch on a new GPU, compared to the same scenario on Flatpak!