I've owned a couple 1841 rifles over the years. The one I have now I pulled the original nipple and the threaded section has a diameter of .259" and it fits tight. I have another old nipple I pulled from a second M1841 (it was smashed down from dry firing) and I mic'd the threads on it and they too were approximately .259." I replaced it decades ago. The one I have now is a hard-used Southern rifle with carved initials and the wood behind the nipple burned out clear down to the screw holding the lock plate. The lock plate is marked N. Haven over 1851 and E. Whitney over US. The barrel bears Harpers Ferry proofs so it was switched during the period of use. There is no US on the butt plate. The smaller nipple is why the tool shown works on them.
It used to be possible at gun shows many years ago to pick up original old stock nipples in different sizes so I kept a few in case I got a rifle that had the nipple smashed and unusable.
I have an extra original nipple for Springfields and the threads mic .308" and one for an Enfield and it mics .309." They have a different number of threads per inch. There is NO way that these larger nipples will fit in the smaller threaded hole for the .259" nipple in the same way that you can't park a Hummer in a spot for a VW. Obviously, no one removed a much larger nipple and replaced it with a smaller one when the threaded hole would have been too large. Musket caps would fall right off those smaller nipples as they were meant for the same caps used on civilian rifles. Many pioneers carried these and other US arms across the plains as Congress authorized the sale of arms from US Armories at cost to those traveling to Oregon, Santa Fe, and Calif.
Perhaps different contract makers began providing these M1841 rifles at some time for the govt. with larger nipples for musket caps in order to standardize all US rifles and muskets for the larger musket caps. That would make sense.
I appreciate the information on BGI carrying those nipple keys. I don't know if Fourteen Old Gun Catalogs has a BGI ad in it but I'll have to look.