Originally Posted by
elcraft
Generally, the rack is best mounted on the most forward mounting holes in the dropout. This leaves the most aft mounting hole in the dropouts for fender mounting. In this way, the fender stays will be shorter and won't cross over the rack mountings. The seatcollar/clamp mount for the rack also promotes shorter struts to secure the rack. In all things mounted a bicycle, "shorter" means stiffer, less prone to swaying, and more likely to stay tightly fastened.
But the rear set of holes gives more clearance between the heel and pannier in addition to lowering the CoG. On my touring bike one fender stay is mounted to the front set of holes and the other stay and rack are mounted to the rear set of holes. When mounting fenders or racks I look at all the options and then make a choice.