This is strictly a problem for the system Python, right?  In that case, can't the dist package clear __pycache__ under the system site-packages directory (and any other user-read-only dirs) during install of the updated Python?

Is the concern that upgrading Python may force all .pyc files to be re-written (perhaps unnecessarily)?  If so, I'm not clear on why it's okay between major versions but not minor ones.  Frequency perhaps?  Is the cost of re-compiling all .pyc files (which mostly won't happen all at the same time) significant enough to warrant changing the status quo, particularly since the magic number rarely changes in a minor release?

As one (poor) alternative, we could require re-compiling a .pyc file only if it contains the affected bytecode(s).  Granted, that would probably require associating every bytecode with a magic number.  The required comparison would likely be more expensive than just re-compiling. :/

Another alternative would be to leverage sys.dont_write_bytecode somehow.