I bet integration is a total nightmare with so many builds and forks out there. I think the version number refers to the build that's running on the ICE/MCU (instrument panel computer), and within that there are sometimes update blobs provided for the other computers like APE (Autopilot), or sometimes vehicle controllers (i.e. VCFront). I would guess that most of the FSD Beta changes would be inside the APE update and they just bump the ICE version number and the only change is inside the APE blob.
APE is its own self-contained system that runs Autopilot, but it still talks to the ICE computer to get navigation data and its the source of all the visualization objects, camera feeds, etc. So it could still be dependent on code that runs on ICE and maybe the newer versions are still not compatible.