Some of the strangeness I found by applying train-miles to Amtrak's financial data in my previous post can be explained with one simple answer: Amtrak considers most of their trans that run in the Northeast Corridor as Northeast Regionals even if they're actually other services. However, it doesn't provide a full explanation.
There are 11 Amtrak routes which run significant distances in the Northeast Corridor: the Acela Express, and Northeast Regional are the core services, of course, but there are also the corridor runs for the Vermonter, Keystone Service, Pennsylvanian, and Carolinian, in addition to the long-distance Silver Star, Cardinal, Silver Meteor, Palmetto, and Crescent.
In my previous post, the long-distance trains already seemed to be either on-target or getting overcharged for the number of seats on the route, so they don't appear to be getting reallocated as Northeast Regionals. However, some routes look significantly closer to reality when NEC train mileage is deducted. In particular, the Keystone Service trains to Harrisburg, Pennsylvania and the Pennsylvanian to Pittsburgh get down to variances of 15 to 21 seats—less than half a carload—so we seem to be able to dismiss those two.
The Vermonter, which was showing only 87 seats through my math but runs 5-car consists, is also helped significantly because 37% of its route is in the NEC. Unfortunately, 87 seats was 74% below my capacity estimate, so only a portion of the deficit was accounted for by subtracting NEC route-miles. The Vermonter also shares about 10% of its total route with a shuttle service between New Haven, Connecticut and Springfield, Vermont which might be used to share some accounting, but subtracting those route-miles as well brings me up to a calculated 166 seats per train. Even a train running 4 long-distance coaches and a completely dedicated cafe/lounge car would be expected to have at least 236 revenue seats.
The Carolinian rides on the cusp of being believable now, about 77 seats away from a previous guess I'd had. A little more or a little less than one car load, depending on the type of equipment used.
But four of the routes I mentioned in my earlier post don't really touch the Northeast Corridor at all. The Ethan Allen Express, Maple Leaf, Empire Service, and Adirondack do share some track in the Empire Corridor, and it appears that some similar accounting methods might be getting used to shift train mileage around in those corridors. Subtracting 42% of the Adirondack's mileage and 67% of the Ethan Allen Express route and adding them to the Empire Service's values seems to at least get the first two services in line, but still doesn't explain the Maple Leaf's apparent overcounting of seats: If I shift train-miles around in the same way, I end up with an outlandish 3,591 seats per train rather than the already impossible 554.