You can move the hole over and up, if it really bugs you, but it isn't necessary, as long as your rod clears the forward lock nail, and doesn't interfere with the mainspring in the lock.
Suppose your rod hole is 3/8". Make a hooked scraper out of some god steel stock like drill rod or the like. You could start with 3/8" rod. In that case, peen the end of the rod to create a burr, and remove all of the burr except along one edge. Insert it into the rod hole with the burr on the side that needs removal, and push it in carefully. Clear the chip/scraping that rises and continue. As you get deeper into the stock, the hole will move in the direction you are scraping. Keep adding 'hook' to the rod and continue until you have moved the hole over enough to insert a different scraper.
This one is made from 5/16" stock, for a 3/8" hole, and has a bend and hump about two inches from the business end. The end of the rod is bumped up like the first tool, and a sharp cutter formed. But this rod will really take out wood. the bent up hump will press against the off side of the hole and the cutter will remove wood in the direction you wish to move the hole. You can even dispense with the first tool, and go straight to the second one. I've used it lots to get the rod hole under the barrel properly.