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I usually do 3-star alignment. Compared to 2-star alignment, I find accuracy improved, particularly in the quadrant where there were no alignment stars.
As mentioned, 3-star alignment corrects for "cone error", which is a summary term for a range of mechanical and optical misaligmments (small ones), not that I'm an expert.
I obviously have some cone error in my setup that others may not have.
My advice is to try both and see whether you get any noticeable improvement from 3-star alignment.
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