Scott
I think the answer to the problem lies in the way in which one homes in on the ideal settings. It is very complex as the motor, prop, ESC and the pid algorithm have to reach a compromise along the way. An example is how a standard off the shelf Phantom quad with default settings works very well yet when you start to play around with different props etc. quite different setting are needed. Loose the mag calibration and it wont fly like it should.
I have a couple of Naza's that get transfered from one model to another so as to create a base line of performance and it is amazing how different they react to a different frame. I would not say that MK is better in my experience.
The offset motor can also be used as a means of creating dihedral which in itself creates inherent stability but overuse can create cross axis errors. I would make sure that the compass calibration is right and has no magnetic interference because this is one of the main problems with the toilet bowl syndrome and yaw defects. The second biggest loss of position stability comes from using big and heavy props. smaller props that are tuned to the rest of the system create the best stability especially noticeable in the descent.
You need to have reasonably locked-in yaw response but don't forget that the overuse of yaw when shooting video is bad so smooth and slow is what you need.