Actually, I think the Confederate Battle Flag will become something like the Imperial German flag IOTL. A Battle Flag is just showing your support for Confederate Independence, which only makes you a traitor in the US ITTL.
The Freedom Party Flag, OTOH, would be far more like a swastika, as the Freedom Party would be unambiguously genocidal, and a Freedom Party Flag is more "I want to kill all blacks" than "I support the Confederacy."
I just had a thought. Since there are now two versions of that flag, how the heck are people ITTL supposed to tell which colors were used from black and white photos and films?