That is just plain wrong. In practice, of the 30+ interstate Amtrak trips I've taken in the past 10 years, the overwhelming majority of them are delayed by freight rail. It is standard operating procedure.
Yes, that's what de facto priority means. Since the railroads operate the lines and the freight trains, they (illegally) give their own freight trains priority over Amtrak passenger trains, which by law are supposed to have priority.
It's actually exactly what de facto means. Amtrak has de jure priority, but freight has de facto priority, because the freight carriers are gaming the system by running over-long trains and other assorted foot-dragging with respect to compliance.