This diagram that I put together may help clarify the views that have been said above. Most software like Sharpcap, PHD2, Ekos use this method to help do PA. As you can see from the diagram, it doesnt matter if the images are being captured via main or guidescope. Its just the radius of the arc that would differ.
EDIT: Added text to explain ....The red circle is what the mis-aligned mount is rotating about and green circle (rotating around NCP) is where it should be rotating about. Our aim should be to get red circle to line up as closely as possible with green.