Hey, now you're talking.
I don't know if you mean to put a dead primer between the flat part of the rod and the primer (this would work).
But your question made me think of a better idea (unless you've already thought of this!). On my RCBS hand primer, the rod that connects to the handle has a spherical indentation in it. This contacts a spherical end of the rod that is used to do the primer seating (if you look carefully, you'll see that your primer seating rods are rounded at one end, and flat at the other - the flat one is that one that should be pushing against the primer).
So here's my idea. If you take a *SPENT* large rifle primer, you could pry out the anvil, leaving you with just a cup. You could place this cup between the connecting rod and the rounded end of the primer seating rod. This would raise the rod enough to allow you to fully seat a primer in one go.
It's not a question of working, it's a question of safety. If the primer is protruding, it will take whatever blows you might give it via rough handling (e.g. vigourous chambering). What you want to avoid is a primer going off because it gets bumped while you're chambering a round. While this is less likely with a carefully handled bolt action rifle than with a semi that closes up pretty smartly, its very much an avoidable risk. Seat the primer so that it is below flush, so the case head fully protects the primer from seeing any impact at all. The only time a primer should experience impact is when it is struck by a firing pin.
(actually there also a very minor reliability point too - when the primer is fully seated, the legs of the anvil apply preloading pressure to the primers explosive pellet. This makes it more sensitive, and is supposed to make for more reliable and more consistent ignition.)