How do we reconcile the two rules, "doubt about performing a pillar is like not performing it" and "doubt after completing an act of worship has no effect," when in doubt about performing a pillar after finishing the prayer?

There is no contradiction between the two principles. The first relates to doubt during an act of worship, in which case one builds upon the original presumption, which is the non-performance of the doubted part. The second specifically concerns doubt after completing an act of worship, in which case the original presumption is its validity, and this doubt is not given consideration. Your question falls under this latter category, so no attention should be paid to the doubt in it.