Depends what you mean by aftermarket air filter boxes? We're not talking about K&N pod filters right.
I have zero problems with modifing things to no end. I love the challange of making things and making them work well. I built my headers from scratch and they work great and sound great and my bike runs fine with individual filters. Jetted at 90/122, Header/filters/500ft above sea level. Everyone has their own vision.
Cheers, 50gary