With my Yamaha HTR-5760 receiver, the speaker levels were set pretty close. For me, I was quite pleased with those results. However, the crossover for my subs were set to 120Hz and a few other "flakes" were noticed.
The chances are quite good that YPAO will set your speaker levels correctly. Once the YPAO process has been completed, just take the time to go back through the settings that were made to ensure you agree with them.
You may very well be fine in living with these results. But, for the rest of us, we still depend on our trusty $35-40 SPL meters for all sorts of sound adjustment tasks.
The only quirks I've had with YPAO on my 5790 were the one that Wayne spoke of(different crossover setting with YPAO from what I went with) and it set my mains to large where I set them as small. Other than that, the level settings and EQ settings were great. All in all, I have no problems with it. It gives a great starting point to work with.