"And nothing has really changed, it can be the BNSF on paper, but there is still a huge separation between BN and SF in the ways things are ran."
Part of that is intentional. The two railroads had some major operating differences, starting with their basic long-haul traffic. The Southern Transcon (ASTF), was, and still is, largely high-speed intermodal. The Northern Transcon (GN), while carrying a lot of containers, is heavy on grain and lumber products. Different freight, different climates, different operations.