Adding to what Jesse has already said, troubles may arise around loose rivets, but again, a diligent shop would notice them and do them separately by hand, or possibly with a pen-sized abrasive blasting gun (which is also a convenient tool for other delicate places and for narrow paint lines possibly remaining at the seams and around rivet heads). Actually, it’s also perfect time to have loose rivets replaced and wet-wing tanks thoroughly checked for any leaks.
As to the filler, it’s normally used very sparingly – e.g. to fill small nicks around the leading edge. I have a larger filled spot on my aircraft, but it still took less than a tablespoon of filler.
Loose rivets should be replaced anyway. They have zero value for the strength which isn’t good. Further will loose rivets give those nasty black stains, which are very hard to remove by cleaning, and come back all the time.
Ultranomad is correct, due the construction method (riveting) an aircraft skin is full of small dents due to the process. Small dents at leading edge can be removed.
