The gauge will be dependent on the railroad, not the jurisdictions. Farmer A being a problem happened everywhere (or didn't, for reasons having nothing to do with the government).
Laws and regulations: Exactly what laws and regulations are going to be more problematic going from Georgia to Virginia than New York to Indiana?
The Feds didn't have much influence on what railroads faced or didn't in the US in the 19th century. Railroads had to work these things out themselves, and did. Somehow.
Interesting, I am hardly a railroad geek so I will take your word for it.