First of all, thank you for the fork and continuing work on this useful library.
I have a suggestion that I use in my own custom version of Brett's library as seen in this project: https://github.com/ptashek/mb/tree/master/CruiseControl_W124 (PIDConfig and PIDController classes)
My approach is to use a virtual getClock() method, which allows me to override it as needed at the point of use. In the project above I'm using RTC ticks as my clock, incremented via the RTC periodic interrupt ISR. It's especially useful in projects which need additional timers, or re-configure the TCA clock, rendering millis() and micros() unusable.
The default implementation could still use micros() as it does now.