To answer the questions, yes it was recalibrated for the Apex, as to whether they were run in is unkonwn, I highly doubt either of them were as they are demonstration models in the shop. I would imagine they take a good amount of listening to before they run in.
I have heard the Apex system in two different stores now and both times, the Sub just did not pack the punch so i dont think its an isolated incident. The advantage of the floorstands is that it handles mid range and carries more weight in its bass, therefore it can leave the sub to handle a variation of others frequencies. The apex on the other hand does not have that luxury and relies on the sub for all its bass, which does not allow you to recieve a full range of bass frequencies. The PV1 is an impressive sub, and the distortion was only heard in oe movie, Batman played superbly. But i agree the calibration could have been off on that one.
Sure loads of reviews say different things, such as the Apex matching a floorstand and beating it, but some of the same reviewers have also said that the Q700 gets 3/5 stars and the Q900 gets 4/5. So i take everything with a pinch of salt.
Ultimately its all personal preference, some prefer a different type of sound. I tend to like the sound to engulf me and suck me into the movie with high detail and resounding bass.