As you well know and the majority of Americans do not, Gettysburg is like most National cemeteries adjacent to or near National Military Parks where major battles took place in that "marked" graves in National Military Parks and National Cemeteries are for Federal soldiers (key word is National). After large and horrific battles such as Gettysburg, the dead on both sides were quickly buried. Sometimes years would pass before the Union dead were disinterred and neatly re-buried in the "marked" graves that we now recognize with the rows of white marble stones we see when we visit battlefields such as Gettysburg, Shiloh, Chickamauga, and even Arlington.There was not any effort to remove and rebury the remains of the majority of Confederates from any battlefield by the United States government. If they were removed from the battlefield, it was years later and the effort was made by the state for which they fought (i.e. North Carolina removed about 3,200 of their dead from the Gettysburg battlefield).
There have been instances where Confederate burial sites have been turned into WalMart parking lots, etc. Even though in 1958 a law was passed declaring all Confederate soldiers, sailors, marines, United States veterans, the gravesites of Confederate dead are not always afforded the protection given of Federal soldiers and American veterans resting in well manicured National Cemeteries. The boys who wore the gray and butternut often lie in unmarked graves not far from where the fell.
I sincerely doubt most ANTIFA know or even care which side was which. Their gammit is hype and destruction 'ala ISIS anyway. If there is an "attack" at NMP's, ANTIFA commies might attack monuments honoring soldiers who participated in those not-so-long-ago battles. By the way, those beautiful monuments, honoring both Confederate and Union soldiers were placed by the states from which a particular regiment, Army, company, etc. hailed. The United Daughters of the Confederacy and The United Daughters of the Grand Army of the Republic held huge fundraisers and lobbied their respective state governments to raise vast sums of money to commission the sculpting of such monuments and having them placed on the fields of honor. We do not need ANTIFA commie rat bastards anywhere near such places.