All in all, longer trains also means fewer trains (hence cost savings on crews for the freight RRs), and fewer trains means fewer meets for Amtrak. So, if done well, longer freights could actually have some benefit to Amtrak.
However, that only works on paper. In reality, you have longer trains that break down, run slower, aren't nimble and block the routes. There is a definite increase in pull aparts, broken knuckles and emergency applications. Now, you have a lone person walking a two+ mile train, attempting to find and possibly repair a defect on the main line.
The delays can stretch on for hours.