I did try rotating the PoleMaster last night. I rotated it 180 deg so the USB port was on the opposite side of the mount from where it had been. Rotating the PoleMaster camera orientation made no difference in its reference star selection during the alignment fine tuning.
Since the axis rotation reference star *is* user defined for the PoleMaster alignment routine, it would seem logical that the fine tuning alignment routine would also allow a user defined reference star. But I can see why it may not -- due to the f/ratio of the PoleMaster camera, for fine tuning they fixed the routine on one relatively bright star near Polaris. If that star is obstructed, you will not be able to fine tune the alignment because there is not any way to define an alternate reference star for the fine tuning routine.
Note, I did finally find a Google result that fit the problem discussed here:
https://www.cloudynights.com/topic/758604-polemaster-and-a-tree-near-polaris-what-to-do/That forum user observed that the same star (Delta Ursae Minoris) is always used in the precise polar alignment routine with Polaris and PoleMaster. The answers are -- no, no way to change it in PoleMaster, but try SharpCap's plate solving as an alternative to climbing and trimming trees or moving the mount to get that precise alignment star unobstructed.
best,
Scott S