It might be a good idea to bring this back to very basic concepts. Why do accounting at all? To assign revenues and costs to activities in order to evaluate the viability of that enterprise and its discrete offerings, such as trains, baggage, cafe, etc...
It is a maxim of accounting to match costs with revenues over as discrete of an offering as possible. IE match ticket sales to trains, stations, and journey segments. Do the same with expenses.
When BNSF looks at a mixed freight train, they want to know where all the freight is going, how much per ton mile, and where the expenses are. The idea is to make sure the train runs in a way that makes the most money, and that the tracks, people, and computers are used in a way that makes the most money.
If an alteration can be made that increases profit, BNSF would likely do so. Why run a train Denver-Chicago if most of the freight runs Omaha-Chicago? Why carry low-profit freight to Grand Forks if it's not enough to pay for the line upkeep? Granted railroads play the long game because the assets are so expensive to build and once gone, they are totally gone usually. But the idea is to run it like a business.
When we talk about Amtrak accounting, it's tough because (a) it will never make money as defined by GAAP; (2) they refuse to change much; (3) the highly political process of making changes, such as diners and ticket offices, makes it hard to change little stuff; (4) they basically will never have competition unless something big happens.
Given the 4 reasons above, management has had little reason to change over the last 20 years, and there's been little attempt to do heavy lifting with accounting.
Its' been interesting following the stakeholders in state corridor and commuter operations fighting over accounting as they all feel shorted, and operators like Keolis have sprung up for a reason.
One of the biggest fights is how to allocate NEC costs. How do you even measure the rates at which the capital costs are allocated? Ton-miles? Passenger miles? Train-miles? Axle-miles? Slots? Each measuring method presents advantageous and disadvantageous facets to various parties. And to further complicate it, they sold off half the NEC to commuter carriers.
TLDR this is a much bigger issue that just "does it make an operating profit".
The new Acela: It's not Aveliable.