Why does RockShox say you shouldn't use a bolt on axle on their fork?
I came to some assumption why you should not use bolt-on axle. 
It is hard to screw the axle preserving fork sliders in one plane. They can get positioned ascrew, because of screwing the nuts in the opposite directions. It is not a problem in motorcycle suspension because of lack of fork brace. But here? let's say you sit in front of your front wheel and have two wrenches, one on each nut. When you tighten left-hand nut, left slider is pulled back by the nut and when at the same time you tighten the right slider, it is pulled forward. Fork brace prevent sliders from returning to initial, single-plane position. This result in suspension that does not move freely, because more tension is put on "fore-surface" of left stanchion.

This "ascrewing" is easy to observe when you're mounting an old fashioned mudguard with mudguard stays mounted on the axle.

I'm sure, that you are able to use bolt-on axle and screw it properly (by using proper nut and spacer and by greasing spacer - nut interspace). Keep in mind, that user/service manual has to be idiot-proof.