To the customer, it often doesn't matter. It can matter, however, in how the revenues are recognized and costs are accounted for. Yes, the money more or less ends up in the same place, but the routing can matter, and the amounts might well end up being different. For example, if there /is/ an adjustment to the fare, the revenue might be shifted to the diner outright and any food order tickets would simply be for inventory. Likewise, a "complementary meal" might end up coming from the "passenger inconvenience" account or elsewhere (if due to a lengthy delay, for example).
So, let me give a few examples:
-A passenger's meal is included in the fare. They board and are on the train just during dinner. For this, of their fare, $25 is allocated straight to the diner. The diner uses its tickets both to check inventory and to check this rate at the end of the accounting period for adjustment.
-A passenger's meal is complementary. They are on the train for dinner. A meal ticket goes in, and the sleeper is "billed" for the cost of their meal should they have dinner (which, in this case, they do), and this is settled up later.
-A passenger's meal is complementary. They were on the train for dinner, and then they were late getting to their destination, so they were also on board for breakfast. Or, in the case of the Auto Train, they were held up by a major derailment and so lunch is served. Dinner is billed to the sleeper. Breakfast, if they were supposed to be on for it, is billed to the sleeper. Lunch, however, is billed to a passenger inconvenience account as a non-standard meal for them.