Alan,
Actually, there are a surprising number of Confederates buried in National Cemeteries. In 1912 the federal government compiled a "Register of Confederate Soldiers, Sailors, and Citizens Who Died in Federal Prisons and Military Hospitals in the North," published as "Confederate POWs Who Died In Federal Prisons and Hospitals in the North," by Frances Ingmire and Carolyn Ericson, compilers (St. Louis: Ericson Books, 1984).
This Register lists many Confederates who died as POWs in the North, and ended up being buried in what became National Cemeteries in several locations.
Geoff Walden