Moby Dick.
What an interesting question. I wonder why you needed to ask it? I thought the FRCs were quite clear on the subject. Or do you know better? Maybe it's just another useful crew-room myth'.
The reason for aligning the 'cyclic stick markings is in order to minimise stresses to the rotor head and mast when running on the ground. Either at MPOG or, mainly at sub-min pitch.
Using the AFCS Controller-test to set the position of the cyclic takes no account of the stress issue and merely sets the arbitrary datum given by the vertical gyros.
So, what do you reckon is the best procedure?