I have set my system up with both a sound level meter and the set-up mic supplied with the amp and get totally different figures, whitch one is better to go for.
Personally that doesn't surprise me. You likely got Audyssey in your Onkyo and depending on the situation when you do the mic-measurements you'll always get different results, both compared to individual measurements and when doing it with a sound level meter. The mic is not really all that high-tec either so who knows how accurate it truly is? Not hacking down on Audyssey as I am myself a fan of theirs, but just saying.
Go with what sounds best. Nothing can judge the result better than you!