I’d suggest to add a sort of flag in Layout files that indicate whether a Custom Design Rule file is used with this Layout or not. It helps prevent possible mistakes that a design is handed over to a customer, where only changed files may have transferred at some times. In a sort of Murphian way, the recipient did not put updates in the same directory as before - in the end, prototypes suffer of real problems.
The result: missing clearances, also those that affect differential impedances on inner layers. Of course, a missing .dru-file should be indicated as a fatal error.