No, If your going to finish it with a solid color- leave the sanding sealer on it. Your going to have to seal any exposed wood before priming anyway. You may as well take advantage of the stuff that's already on there.
There are several spots where the existing sealer has been removed. What do you recommend I use to fill those spots flush to the existing sealer before sanding it all? Whatever I use, I want to be sure that outlines of the holes I've filled won't appear after the final paint job cures.