That's what I originally thought and when I got my Yamaha 4600 I played around with the YPAO or whatever it is. I couldn't switch back and forth quickly to determine if it was better or not and left it for awhile...after tinkering for awhile. Then when I had a guy over for a demo I turned all EQ and such off so the speakers were in their natural state and left it since.
Perhaps if I ever get the house to myself I will need to explore some more and learn to copy and use macros on the receiver remote. Or perhaps the harmony 880 would be easier?
I could have sworn though that I've seen lots of posts about not using the Eq's. I'll need to start searching the site.