Don't trust the Wiseco box I think they let there kids do the labels. But this time they are close. Clearance is directly related to type of piston. OEM were cast pistons, cast pistons due to there ratio of silica/ aluminum don't expand as much as forged pistons like Wiseco. So the manual is only relevant to cast type pistons from Suzuki or art etc...
The new generation of Wiseco are much better than the old pistons from 10-15 years back. I used to set up with .005 " clearance to be safe. But it was hell on piston life and boring cylinders. I now set up at .0035"  and spend more time on break in.  During break in you actually size the piston to the bore. What happens is you go through a progression of heat cycles continually hotter. In doing this the piston expands during operation and obviously cools when you shut it down. These Cycles actually end up shrinking the piston slightly also the skirt of the piston collapses. Of the two the places where the piston shrinks the crown is the one that losses less size  it has the most mass but also the most support so it hold s it size better than the skirt.
The skirt on the pistons are the weak point due to lack of material and poor rod angle. So on a new engine once the skirt  collapses and you have sized yourself on the high side of tolerance. You can end up with excessive clearance. .002" can be the difference between a long service life and one that's noisy and will need to be bore every year after only a few trips. In the end you need to maintain the piston properly. Good quality oil and more is better. Its the only  cushion between the piston and the cylinder if its not there it can't work.

Moral of the story proper break in is critical. And proper warm up is crucial.But don't go less than .0035" on a 500 or you run the risk of seizure.