Just to be clear, most of the pre-flex "traditional dining" meals (except the steaks, and maybe a couple of breakfast items) were not "cooked to order." Even back 10 years ago, when the food was a lot better, most of the entrees were pre-made. The big change (aside from the quality of the entrees, which could easily be rectified) is in the presentation of the meals. "Traditional dining" provided an illusion that you were being served "fresh cooked food," whatever that is. However, it did require a full dining car staff to heat, plate, and serve the food. Under the flex system, the meal is heated and served in the same platter, and thus, the passengers can be served by dining car staff of 1. (Maybe have the coach attendant help out if there are very high passenger loads.) That's where the costs savings come from.being used to the old cooked to order meals it was a big disappointment.
It is entirely possible the the marketing people at Amtrak know what they're talking about regarding millennials, who may not value food presentation as much as previous generations, just as we boomers drifted away from the bourgeois formality of white tablecloth, fancy china and silver of our parents. (This is course is a generation, and there may be millenials who prefer traditional dining, as well as boomers who yearn for some bourgeois formality, but that stuff costs money, and there is a clear trend of most consumers opting for affordable prices over fancy presentation.) The growing success of fast casual restaurant concepts at the expense of sit-down "white tablecloth" establishments might be evidence that this is the case.
Maybe 30 years ago they were still cooking everything in the dining cars, but they haven't been doing that for a long time. I don't know the history, but they've been cutting back on staffing in the dining cars for quite a while. The "flex dining" is just the culmination of this process (*) -- now they don't even need waiters. Personally, I really don't care, except that I'd like the food quality to be better and the service to be fast, efficient and friendly -- no long waits for food and being able to sit in the diner-lounge and eat undisturbed by OBS staff who are frustrated boot-camp drill instructors. I don't even care if different trains have different procedures for serving food. These may be justified based on the circumstances of the trip. I'd just want OBS staff to make it clear what the procedures are.
(*) Well, maybe not. Perhaps the culmination of this process is vending machines. Or maybe even just a lounge car with a passenger-operated microwave oven for passenger-provided food, if they can get the applicable regulations changed. Or maybe platform-side vendors. )