Audyssey is very accurate, if the measurements are taken correctly in a silent room. Position is important, for ex, you don't want to take measurements "outside" of the speakers locations, you need to be "within" a bubble of the seating locations.
Also, it looks for the -3dB point of each speaker and reports that back to the receiver. So it is not suprising if you mains and center get a "large" or low frequency reading. But, even Audyssey says if the receiver, not Audyssey, sets a speaker to large, if you have a sub, you should change that speaker to "small" and possibly bump up the crossover to 80hz. Never lower a crossover setting.
The dB level readings, as well as distance is not big deal if they are slightly different, all rooms are different.
