I can not comment on how well the eq works when compared against a manual eq but I can comment on how accurate the YPAO is in other areas.
Speaker size - If you have decent speakers it will probably set them to large, which requires going back in and changing it (unless you don't have a sub).
Speaker distance - It nailed it in my room.
Wiring - There have been some reports of it incorrectly reporting speakers as out of phase, just double check your connections if this happens.
Speaker Levels - It was very close in my room with the speakers being set a little hot. My speakers were set about 1.5 dbs high across the board with "0" being dolby reference.
EQ - I have found that the EQ does improve the sound in my room without hurting imaging or the soundstage, you can hear a big difference between each eq setting. Flat worked best for me but if you have "bright" speakers or a "bright" room natural may work well.
I know I didnt really answer the OP's question (sorry) but wanted to put this out there for those interested in how well the YPAO works.