I have seen several original .25-20 caliber Model 1889 rifles. At one time, I went through the records to find all the serial numbers of those particular guns, which is why I know all of the .25-20 caliber Model 1889's are deluxe with pistol grip stocks (besides the note in the 1894 Marlin catalog stating so).
As far as barrel changing goes, it could be done by a gunsmith or returned to the factory. Usually, if a gun was returned to the factory, a second ship date was listed for that particular serial number.
The factory would not have made up a special stamp for barrels that were shipped to gunsmiths to install. Roll dies were expensive to make, and cost of the extra roll die would not be worth it. Besides, what difference would it make, so long as the gun had a Marlin marked barrel in it. There are a number of places in the records where a serial number is listed, and all that is listed is "Trigger plate". Which means a trigger plate was shipped out to replace one that was damaged somehow. (such as maybe a horse fell on someones gun and broke the stock and trigger plate)
Due to the increasing cost of ammunition, there be no warning shot!
The growing federal deficit = generational slavery to the national debt.