How could that be true??? The Ball is leaving the muzzle at whatever muzzle velocity you have loaded for the caliber, often in excess of 1200 fps. Do the math. Just how long is it going to take that ball to go past 2 inches???? And that rod sticking our past the muzzle is still at least one caliber size distant from the ball in most guns. I can see there being some problem if a Flat surface was near the muzzle, reflecting back gases, and air to the projectile as it passes, but the rod and jag are round, and cannot reflect back anything of significance. If you must, do some before and after testing of your gun using a bench rest.
I keep a loading/cleaning jag on the end of my rod, sticking out beyond the muzzle. It gets coated with greasy residue, but that is easily wiped off with a rag as I pull the rod out of the stock and pipes. If no rag? A handful of leaves, green, or dead, will accomplish the same thing. I keep 3" squarer cleaning patches made of flannel cotton in my pouch for cleaning the .50 caliber, 20, and 12 gauge barrels on my guns, so a couple of those patches also can be used to wipe the ferrule and jag on my rod as I pull the rod out.