The current configuration design is that user .idlerc config-x.cfg files contain changes from the idlelib config-x.def files.  A proposal to change this is an enhancement request rather than a bugfix request.  It will make the logic more complex, increase maintenance burden, and likely make changes to the configuration system harder.

If Python is installed for one user, any changes to config-extensions.def only apply to that one user, just as with additions to site-packages.  If Python is installed for all users, why shouldn't extensions be available to all, just as with additions to site-packages?  Assuming that extensions are by default not enabled, users will have to explicitly enable them, just as they have to explicitly import added packages.

On a system with non-admin users, such as in a classroom, I can imagine that the admin user(s) might not want non-admin users to be able to modify IDLE behavior.  I am reluctant to open this can of worms and would not do so by myself.