Perhaps it's my fault, I am not getting the point across properly. Yes, I realize the star alignment done on the hand controller does not physically alter the polar alignment, since there are no servos on the RA and Dec knobs. I am just trying to figure out how does the controller deal with errors in polar alignment, whether it can actually detect them during the star alignment, and whether it tries to compensate.
Let's say you do polar alignment with the polar scope. It's close, but no cigar.
Then you do the full 2+4 star alignment with the hand controller. At this point, the HC has enough information to estimate not only the various offsets, but also the real orientation of the whole mount, relative to the celestial sphere. It could probably estimate PA errors too, I presume. Does it apply corrections based on that estimate?
Or does that become part of the cone error correction? In other words, does the HC think "PA is assumed perfect, all errors are due to cone error", or does it think "I am detecting PA errors, let me estimate the real orientation of the RA axis and use that instead"?