Drew is saying that it's only against the rules if you get caught. If you are the only bike running in a class there probably won't be much protest if the mod is not obvious. But if the scrutineer spots it in impound after you record and determines it's not legal you have a problem. My teammate was put into a state of anxiety in scrutineering last year because the scrutineers were somewhat split on how to measure the maximum height that a seat hump may be above the rider's butt on the seat in Modified. This anxiety was over about 1/8" of height. In the end they determined it was legal. I remember one year when Hiro Koiso had to chop about 1/4" of the end of his rear fairing to be legal overall length.
It pretty much boils down to whether you think you have a chance of setting a record and how much the mods might help. If you need 5 more hp to get a record and smoothing your inlet tract might be illegal but gets you 1 hp it may not be worth the effort if you can't find 4 more hp elsewhere.