Mounting the top box directly over the passenger seat works great. I fabricated some brackets for my VFR 800 that I had, and made up 5 more sets for friends. The box has little to no pendelum effect in that position and can also be used as a backrest. I have never been found of factory mounted bags, and having the top box mounted up high and over the tail, always seemed to ruin the handling when riding aggressively.
I will be making some brackets this spring for my Versys. I too, had to remove the bracket, to get under the VFR seat, but it was only minutes to remove it.