You are right. Another choke point was the increased loss of draft animals to the army. The drayage needed to haul trainloads of supplies from one side of town to the other was in critical decline. No wagons & miles, no rail road.A few years ago, I came across one of John Keegan's books about the CW. One chapter in particular intrigued me. I discussed the South's RR's. There was a map that at a single glance explained the South's deficiency. What we would think of as a simple route from a to b was anything but.
When Longstreet was dispatched to reinforce Bragg, you would assume a simple direct route due south to Augusta Ga then straight over to Atlanta and finally straight up to Chattanooga. There were gaps which would have necessitated detraining and marching to pick up the rail again. At least some of the troops and equipment would have swung all the way to Charleston on the coast. Not to mention that due to the differences in track gauges, even if there was rail coming into and out of a given town necessitating completely unloading and reloading all the men and supplies.