Fred Frailey wrote about the 3-sets-of-books issue in his 1998 volume "Twilight of the Great Trains." I found the chapter on SP and their use of a thing called form 3646 especially interesting. As long as a train was covering its direct costs using that yardstick, management kept it going. Only when a train slipped below that did SP start to assemble a train-off case; then the fully allocated cost method was used.

Anyway, if Amtrak was close to turning a profit, I think the freight railroads would have seen that developing and ponder whether they wanted back in or not. After all, most private businesses don't want the government (or a government sponsored entity) operating on their turf. If they had a choice between continuing to have Amtrak as a tenant or running trains of their own that hovered around the break even point, what would they do?