I think you hit the nail on the head. Since your setup was closer to optimal than not, Audyssey did not have that great of an impact.
When I had the Denon 3806 from a few years ago (forget which version of Audyssey), I preferred Pure Direct. Now with the X4000, I cannot imagine using Pure Direct. As it happens, the room and speaker arrangement with the 3806 was much closer to optimal than my current setup.