Just how many National Cemeteries are flying the Confederate Battle Flag? Can’t be that many, if any at all. This looks to be a solution in search of a non-existent problem.
Maybe he meant National Parks. I don’t know of any Cemeteries that allow it on a daily basis. Even the US Flag is on a flag pole in the Veterans section.
This is the only hit Google brought up
http://www.dispatch.com/content/stories/local/2015/07/09/confederate-flag-federal-cemeteries.html