Back in the "good ol' days" of regulation, rates were essentially set by the ICC and revenue for shipments over more than one railroad split by a (sometimes complicated) formula. Lots of clerks, lots of paperwork, lots of lag time between work performed and payment received.
Revenue might be split by mileage, but usually that was too easy. The office also had to calculate per diem and demurrage, and probably car repairs handled offline.
Small railroads didn't have their own settlement offices, and relied most often on the Class 1 to which they had their primary connection to perform settlements.
Parallels existed in communications (telegraph and telephone) and pipelines (oil, gas, etc.) and still do in some ways (intrastate settlements between the former Baby Bells and the "independent telephone companies" in their regions being one I've worked with, and very close in concept to the Class 1 - Shortline relationship).
JAC