My youngest was like this too - he had to be naked to use the potty, for whatever reason. We just let him. The funny thing is right at that time we were potty training him, he also happened to have this obsession with these snow boots that we had just gotten him. So at any given moment you'd find him sitting naked on the pot with his snow boots on.
As for the original question, the run free and naked years ended about 4 years old around here.
Both of my boys are modest now, sure would have never known it when they were babies though!
