As the judge in this case pointed out, Amtrak is a PRIVATE CORPORATION not the government. Just because the Federal Govt owns most of the stock doesn't change that. That said, they do (as do other railroads) have the power of eminent domain, and I think they actually used it in at least one case - failing memory mutters about something in New England/Vermont maybe? It was a long time ago. They don't like to do that because it costs Real Money out of This Year's Budget that is difficult to fully prepare for (eminent domain means the govt or other group authorized to do it (RRs, utility companies, pipeline companies, etc.) can take property against the owner's will, but they have to pay market value and the courts will determine that if there's a dispute). And of course it kind of poisons the relationships with the affected railroad and many others that Amtrak needs to maintain to keep running trains.

What this case does is strengthen the hand of the UPs of the world. They don't have to worry any more about being beaten up by regulators about treating Amtrak badly in the dispatching room; judge says that can't be done. Of course, if they have a CONTRACT that specifies a priority or other level of service Amtrak can always take violations to court and try to collect damages. Didn't some commuter line running on one of the big RRs do that a few years ago? Good luck - the one with the most and most expensive lawyers will usually win.