Based on what we know about direct costs (revealed in Boardman's presentation), by which measure the LSL does very well, the LSL's "poor performance" is due *entirely* to getting an unusually high allocation of "allocated costs" compared to most long-distance trains. I see no easy way of determining where the allocated costs are coming from, since Amtrak cost allocation is a black art.
I would honestly like to see an "avoidable-costs only" report, but Amtrak publishes those extremely rarely.
Analyzing these trains is tricky because no two are alike.
It's worth noting that the LSL is a train where over half the dining car patronage comes from coach passengers, which is apparently unusual for long-distance trains. (Information from the PIP.)
Regarding fares: It's also a train whose main market is upstate NY to Chicago. (Also from the PIP.) I don't know if you've ever tried to get a Greyhound from upstate NY to Chicago -- you literally can't; you're put on connecting buses from other companies (various "Trailways" affiliates), with even worse service than Greyhound. The direct buses from NYC to Chicago, of course, do not go via upstate NY. It makes for a funny situation when you're trying to compare fares. I would expect Amtrak to be offering prices which track the bus prices pretty closely in the core upstate NY - Chicago market (which they are, although the bus prices keep going up faster than the Amtrak prices), while selling the NY-Albany leg fairly cheaply to fill up any unused capacity.