Yes, the freedesktop runtimes ship extensions with newer versions of Mesa and its dependencies. This doesn't entirely solve the problem. For one thing, libstdc++ before GCC 5 did not maintain a backwards-compatible ABI, so if the app was compiled too long ago it won't work with a new libstdc++. Steam is now working around this problem by using dlmopen() namespaces to load different version of libstdc++ into the same process. Flatpak is not there yet.
For another, NVidia drivers complicate this even more. The NVidia client-side library must exactly match the version of the loaded kernel module which Flatpak can't control. So NVidia drivers are broken out into yet another runtime extension, and it can't package these drivers due to licensing issues so it will dynamically download NVidia drivers to generate an extension on the fly. NVidia drivers also depend on libstdc++ by the way, another reason why static linking doesn't magically solve the problem.
On top of all this is just the massive complexity and maintenance burden of keeping all this working. All these runtimes with all their extensions, somebody has to keep updating these, and when a runtime is deprecated all of the software that was built for it is defunct. All of this can be solved just by keeping libraries backwards compatible and building for native Linux, not Flatpak or anything else.