RE: "Natural Sound"...
It could be that the Yamaha is actually neutral, and that other amplifiers are coloured in a way that is more pleasing to the ear. IMO, neutral amplifiers sound unremarkable. This might be what the "natural sound" is all about. But this is only speculation (however, Yamahas get great reviews in AVSA all the time, so they can't be all bad, right?).
Also, on YPAO: you can tell the amp to keep the mains standard and match the other speakers to the response of the mains. In fact, if I were troubleshooting this setup, I'd turn YPAO off altogether and start from there. It is best to sort out the system acoustically first (via room treatments) and proceed from there.