Again, lets not cloud the water for others!! Why must people make mountains from ant hills here on this site? A basic question was asked by the original poster, and he was given a correct answer, the correct factory specification answer! end of discussion!
The entire reason yamaha made the powder forged piston was to run a TIGHTER skirt to cyl wall clearance, this provides BETTER ring seal and BETTER piston stability, the piston does not expand rapidly like a wiseco forged unit does!! Running it looser in the bore is completely wrong, you lose performance that way! a looser skirt to wall does not make the engine any less prone to squeeking a piston, thats from incorrect warm ups and /or lean jetting! The std wear limit is .002"-.0027", pretty simple, will it still run if looser??, sure!!, is it to factory specs....NO!
If you want to make specs other then what the factory reccomends for yourself fine, but dont cloud the water for others trying to learn the basics. For first timers your making them feel like its something they cant handle and its quite the basic repair, or preventive maint.