My point is more about consistency, Audyssey/Denon/Marantz design the system as a whole, and Audyssey would configure the filter set based on measurements it collected from the Mic/room/speakers/placements. So if you change one variable, the results will no longer be optimum, though I would say any such difference would not be audible. So why waste the time, that's about it.. I respect Gene and Theo, but I highly doubt they have spent as much time on playing around with Audyssey and REW like some of us users so they may not have the practical experience that we have.
Also, it is the end results that count, people like me, and
@Pogre managed to get our in-room response to within +/- a couple dB from 20-120 Hz without smoothing without using anything other than the stock mic and run Audyssey following instructions, though we did use the App to do some fine tuning after. Check out more curves we, and others have posted in the Audyssey editor app user thread if you are interested and you are welcome to post your results for comparison and exchange ideas for improvements.