As long as you had the SPL meter in the EXACT location left/right/height and orientated straight up, I can see your concern, the SPL reading should be the same. However, the dB levels on the receiver might be a few dB's different to achieve the same reading.
In regards to the sub that is strange as well. My EP350v3's using my old Denon 2805 setup give me the exact distance from the sub's voice coil on the driver to the mic. Now the EP600 is another story, because of the DSP, the receiver puts my 600 about 10ft further than it actually is....I don't have Audyssey.
