The closed loop steppers are wired to the breakout board just like open loop steppers. The loop is closed in the drive, and the UC300ETH never sees the encoder signals.
Depends on how you wire it? If you wire everything in series, maybe as few as 2? Or as many as 6 or more?I have seen about using a combination of limit switches plus the home/Z pulse on a closed loop stepper as a way to accurately home. How many inputs would be required on my BoB to account for this?
Note that you'll need to write a custom homing macro to do this.