Unless you suspect corrosion underneath, taking it down to bare metal isn't really necessary. If you can feel confident that you have a good base that's the most important thing. If you need to take it to bare metal to sleep at night then that's not arguable, and when there are multiple layers, and signs of filler, taking it all the way down is the only thing left to do.
There's been many many times that I find filler on a car and was completely surprised by it. If the body guy is good, filler isn't a bad thing.