Not wishing to beat this to death, but this is absolutely a military conversion for military purposes, probably done by a civilian contractor, but possibly done at a federal facility. In any case, you have misinterpreted Schmidt. He is describing the federal program for altering certain federally owned flintlock arms. A totally different set of criteria applied to the huge stocks of state-owned arms in state arsenals, or to private armories owned by private uniform militia companies. All of these were invited to have their flintlock arms altered at federal arsenals, for a price. This led to unexpected problems due to a lack of hammers to fit pre-1822 patterns of Muskets, 1803 pattern rifles, and Kentucky -style rifles, of which there were many in state hands. There is some interesting correspondence concerning assorted contract long rifles owned by Virginia. Washington Arsenal declined to convert them, but offered to have them done at Harper's Ferry where hammers could be individually made and fitted. Virginia agreed to the extra cost and the rifles were presumably altered. Finally, when it was clear that Lincoln intended to invade the seceded southern states, there was a rush north and south to alter remaining stocks of flintlock arms of all types. Contractors in Virginia, North Carolina, and Ohio are known to have done this type of alteration in 1861, and countless there were others.
The military style of the hammer, the presence of a military musket cap cone, and a bore reamed smooth all indicate this was a military job and this particular arm is very interesting to military collectors, even if it has only marginal appeal to long rifle fans.