My guess is its a birth defect. I know some breeds have a more rounded bridge on the front of the face but that looks more like a defect. As long as there are no physical limitations and it doesnt bother your horse and you love him I wouldn't worry about it.
It looks to me like it's a birth defect or an old injury where he would have hurt himself quite seriously. I have never heard of a breed of horse which has what your QH has. I assumed you were initially talking about a Roman head which yes, tends to be a breed thing.
What I find interesting is that he must have gone thru quite a severe injury to have bumps like that but there are no scars or obvious external signs of an injury which would tell me it was a birth defect??
If it was an injury, it's crazy he would have something like that and no one even knew anything about it.