If the Confederacy had won it would have set a precedent. Yeh and if pigs could fly I would always wear a hat. If any evil regime wins it set a precedent. The Russian Revolution won and set a precedent for the creation of other evil regime, so what. Luckily for America the Confederate pseudo state was defeated.
States only have “supreme powers” in those areas they are allowed by the Constitution. Areas markedly prescribed by later amendments, the 14th in particular. Because of this their powers to control for example elections and education have been limited. If the Framers had wished they could have stated the right to secede, but they accepted that this was “perpetual union.” And the Supreme Court has consistently accepted that view that we are “an indestructible” union.
Pardons and paroles, again. They were just part of a reconciliation and let’s face it. All kinds of scumbags get paroles and pardons, rapists, child molesters, murders, politicians and in the case of the Confederates, traitors. The veterans’ action was biggest meaningless gesture of all. How many of the million Confederates that survived the war, heard or saw that. They were food for worms by then. The Union soldiers saw financial benefits for their service, not the traitors.