Since the auto (turn on) feature for sub is signal based I would turn them off but more importantly and a
must do is unplugging the rca's from either the sub itself or receiver. I'm sure it's easier just to do it at the sub amp. You want YPAO focusing on your mains and rears/surrounds only.
Use the mic engineered for YPAO from Yamaha when calibrating and i'm sure you will but just wanted to be sure. I've spent a bunch of time e-mailing Yamaha engineers about the supplied mic and YPAO boundaries. It really is a good system and when I upgrade to the Aventage 3000 receiver that will have their best calibration system with the ability to see what its fixed and adjust off of it by taking the Parametric calibration and then copying it straight into the manual side and tweak till your hearts content.
Sourcing a better mic for REW is always good and the Dayton mic is a good choice and wife friendly (cost), fwiw. There appears to be a lady in your life based on one of your pics, how does she like them and curious what her first reaction to them was???
If I could just figure a solution for the WAF... I would be a rich man...