I got the JP video off google video and in it he addresses both ways. His explanation for it is that it yo should be able to do both well so that in any situation you will be able to pick it. I think this too, however I play most naturally with out strict alternate picking either. I don't see a reason for it. BUT to warm up my right hand I do strict alternate picking exercises, especially with string skipping, this has helped a lot in picking accuracy and the speed at which I can move my pick around.
SO practice both, play what feels natural. Thats what I would say.
