3 star alignment is just for your goto to improve pointing accuracy. If your polar alignment is out the goto will still work but the image will slowly drift in the dec axis (for visual and when only tracking), guiding will be working hard to keep up and you will get field rotation in long imaging sessions.
Good polar alignment is needed so your mount doesn't need to make a lot of adjustments to the dec axis so you get smoother guiding and sharper stars.
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