Maybe because on aftermarket rearsets the footpeg tends to be higher, less likely to touch. Your also not going to fold your foot up into a solid footrest when right over.
One of the reasons I ask is because I do a LOT of city riding and every time I put my foot back on, I have to readjust it. I have to lift the leg twice because it's spring loaded. It might sound like a small thing, but my leg muscle locks up after about 4 hours of riding.