You are correct - if you buy into the goal of the Audyssey target curve (which is not totally flat btw) and EQ you have now deviated from it into a preference. But you have still not strayed far from all the benefits of Audyssey Room EQ and Chris from Audyssey did not really go to any lengths to discourage it. I use the PGM2 tweak myself.
I am SHOCKED at this!
I know you place little value on my measurements, but here is exactly how far you stray from Reference with Pgm2: