Aha! The villain behind these super long trains is Precision Railroading. Longer trains mean less crews which means less paychecks which means more profit for shareholders.
Freight traffic logs more miles consecutively across the US than Amtrak ever could. Plus, freight carries goods and products totaling Billions of dollars every day. Which is more important? Since no one seems to be interested in solving the infrastructure problem, I don't see Amtrak sticking around much longer.
I've worked for a RR. If a psgr train waits in a siding, the opposing freight train rolls by at full track speed. If the psgr train holds the main line to allow a long heavy freight to enter the siding at slow speed, the delay to the psgr train is much greater.
Because AMTRAK doesn't own the tracks, they use ither railroads trackage, and unlike AMTRAK those other railroads must turn a profit to survive. So the freight has priority.
The fact that Amtrak now is experiencing frequent and repetitive mechanical breakdowns on it’s long distance routes isn’t helping things. Amtrak crew terminals are much further apart than the quoted 90 miles for a van re-crew. The host railroad also has to come up with a freight locomotive tow as well.
Probably some of these federal rules need to be relaxed. Let the engineers use their skills without constant fear of PTC "penalty" braking. Congress has basically imposed contradictory requirements on the railroads, and something needs to be adjusted. Or, ban the running of trains that are longer than the passing sidings.
Easy fix. Prohibit trains longer than the shortest siding. Create more railroad jobs. Think of it as payback for all the land and money gifted to the railroads for the transcontinental railroad.