I've heard that it is bad to use a Japanese maple as a bonsai if it is grafted to a different root stock. (different growth rates, grafting scars, etc..) My understanding is that most Jmaples are sold being grafted this way.

My question is, if you would airlayer above the grafting line, would you avoid this problem? Am I correct to assume that the trunk would grow its natural roots, allowing me to cut it off and allow it to grow naturally?

If you air layer above the graft line you will be dealing with only the genetic material of the tree. So any new roots generated above the graft line will be of the species above the graft line. If you are successful with your layering you will have eliminated the issue of uneven growth after you remove the bottom, grafted portion. Hope that helps. Good luck with your air layering!