Indeed, Dillon is a strange beast, full of issues, while being basically great.
One issue you touched upon is interferences between the handle and the bench. In my case I was able to work around them by making one extra part - special bushing for the handle, eliminating the extra protrusion on the bottom. That protrusion tends to hit the nut on the mounting screw, and there is no other way around it. Such interferences are unfortunate in the product of that caliber.
Another issue - a not consumed primer slides down the chute and often falls on the floor. A simple addition of a piece of plastic tube takes care of that. In this case - a tube used to package the IC's worked great (second picture)