I did a bit of a deep dive on this over the weekend and left feeling more confused than when I started. From what I can gather, outside of CN's holiday freight train, most of the tracking is done by community members with SDR antennas and Raspberry Pis. They report to centralized servers (which I've yet to find), and the data indicates where trains are in signalling blocks. I'm the least knowledgeable person on trains, so I don't know if this is all accurate, but that's my best understanding.

I'd love to build some sort of service that takes this data, references a DB of signaling blocks, and establishes an estimated lat/lng - but that's a huge project of its own.