I bought a Honda OEM top rack for my VFR second hand, rack only, nothing else. I've got it installed over the OEM sidecase stay kit ok (Well, after one snapped bolt removal) but I've noticed the bolt heads are a bit off-center in the recesses even though all the bolts threaded properly. Is this normal? Also, I installed it without the short collars, which I was told were not needed with the OEM stays in place...
You seem to have it installed correctly, the bolts do not align perfectly, and I didn't use the short collars either, as I didn't have them.