While I'm aware that FEC does run, more-or-less, a scheduled railroad, my observations of a local regional railroad that makes a huge effort to schedule its operations (and doesn't have Amtrak to worry about, save for joint operations on the UP and BNSF) shows that it's more difficult than you think.
The FEC has a lot of captive hauls; it controls the movement from point 'A' to point 'B' and everything inbetween. It's essentially a dead-end railroad so there's only significant interchange at one end of the system, and it's pretty easy for them to say "well if CSX doesn't pull their train into our yard on time, we're going to leave, and those cars will just wait until later."
On my regional railroad, if UP doesn't deliver the cars to Eugene Yard, there is no train. So maybe the road will have the crew do "clean-up" work to keep busy. The problem is that those cars are out there and will be handled, just not on schedule.
The next day, the cars show up, PLUS the cars that are supposed to be on the train. You now have a train that is heavier and longer, takes longer to get to Albany, takes longer to sort in Albany, and won't fit in sidings. Congratulations, the crew is dead on the law. You now have to pull a crew off another train, taxi them to the dead train and have them bring the train in. But that other train is tied down on a main track somewhere not going anywhere. Meanwhile, the yard is clogged so at least two or three other trains are now delayed - all because ONE train didn't interchange properly.
It's also very hard to tell a customer "I'm sorry, but your cars didn't make the train on time, so they're going to be delayed by a day."
Back on the Class One, what do you tell a unit grain or coal customer, or a solid TOFC/COFC or auto-rack train when it's time to go and only 3/4ths of the train is loaded? Do you tell the loading crews to stop work, the train has to go?
I'm not saying that all of these matters can't be arranged or done, if handled right. Obiviously FEC and CN is doing something right. But keep in mind that FEC doesn't host Amtrak, and CN hosts, what, one Amtrak train (City of New Orleans)? Maybe those two examples aren't the best to use in this context...