I wouldn't worry too much about this. While the manufacturers efficiency may be coming into play, the goal of calibration was to even out each independent set of speakers so they are playing at the same levels in order to get the most accurate surround effects and soundstage.
So your Aperion's got correctly calibrated and then the Axioms got correctly calibrated. I see no need to compare the results of the individual settings used against each other unless you are concerned about pushing every ounce of power out of your receiver, also known as "going deaf".
For the second question, if you are trying to compare the two speakers, then you should be listening at the exactly same volume levels. Otherwise, as people have mentioned, people tend to naturally favor a louder sound.
This is where a db meter actually comes in handy. Both sets of speakers are calibrated to be equal among themselves, but as you have discovered, to listen to each set exactly at the same volume level for testing, requires an adjustment on the volume knob.
If you are just talking about what volume levels you should listen causally at, then listen at whatever sounds best to you.
