Maybe the problem is with YPAO.

In my instance I use MCACC for EQ calibration. I do not use the distance or level checks. I do that manually.
After EQ calibration I can play this demo bouncing ball that jumps from one speaker to the next and as it circles the room it sounds tonally correct and balance. Before calibration the ball sounded differently from the mains to the center and the rears. I do not agree with Alan Lofft in his view of calibration for Home Theater at least. I can see his point in relation to music. A balance properly calibrated video and sound presentation in Home Theater can provide a much more enjoyable experience. As with my example I have different sets of speakers and sound tonally mismatched. The MCACC in my case blends those speaker quite nicefully for home theater. Yes this inadvertantly may change the FLAT responce curves of my Axiom QS8 and VP150 speakers but the general presentation as a whole in MY setup is much better. The Elite series has a button than can disengaged the MCACC calibration. I do that when I listen to music.

I personally think that even the VP150 and QS8 tonally sound a little different. Try playing your test pink noise with the VP150 and QS8 and toggle back and forth. I would be astounded to hear you say "Oh they sound the same". If they sound the same why are not people running QS8 for a center channel? They are both FLAT and they sound the same...so why the hell not.

I share your same view that like YPAO and MCACC are great and help lots of enthusiasts but the software still needs to be refined. As with systems that have all of the same speakers coming from the same manufacturer and have the same drivers there is usually no need to EQ calibrate the speakers. But for systems that have different set of speakers from different companies...EQ calibration can help quite a bit...or not...

As there are GREAT people on this forum that PREACH GREAT DOGMAS. All opinions on here should be taken with a grain of salt. Some are wrong and some are right. Try it out for yourself and come to your conclusions.