I agree, that little extra move to get final alignment doesnt look right, partly as you say, because the movement is unequal in the different rotations, from my simplistic, completely non cnc point of view, could there be some small amount of slop in the servo drive system, like a slightly loose pulley, or a partially sheared key, caused by the machine crashing, which the alignment system is compensating for, I suggest this because many times in my life, looking for a complex answer to a relatively simple problem has always come back to bite me in the arse, especially if I have assumed that the fault always lies in the most complex part of the system, ie, the damned electronics!
Phil