OK, you have a point, but neither the purchasing agent nor the bean-counter supervisor is considering the cost of the labor to heat up and dish out the stew and clean up afterwards. On the other hand, because it's not on their account, they might not care. The advantage of MREs is that they can just be passed out with no further involvement by crew, who might be busy dealing with other aspects of the delay situation. There is an advantage over KFC and the like because the cases would be on board, stored in the baggage car, and would not require someone spending time arranging with the local KFC or whatever to order and deliver. This might be especially useful if the train is snowbound, stuck in the Donner Pass.
The labor is already a sunk cost as long as an LSA, SA, and chef are on board. If the conductor needs their help in an emergency, well, first things first.
Remember the premise of the OP. About 350 hungry passengers, no relief in sight, and normal emergency stocks (whether Dinty or MREs) are exhausted. Ok, so you propose that additional emergency stocks be carried in the baggage car. Given the points above of cost and ratio of actual food to packaging, does it make better sense to carry a few cases of seldom-used MREs (which, although shelf stable, do keep best in a temperature controlled environment) or the equivalent volume of additional Dinty and rice?
Look, when a train gets into this situation, no passenger is going to say, "Wow! I got an MRE!" (Waitaminit, there are some AU types who consider eating the Dinty Moore a badge of honor!) Realistically, though, the best any crew is going to do in that situation is shift some passengers' attitudes from, "Never again!" to, "I guess they really are trying to make the best of a bad situation." And to that end I'd suggest a high-limit credit card for the LSA and a database of every restaurant, grocery store, and take-out place along his route.
Editing To Add: Keep in mind that if you want to serve just one MRE meal to 350 hungry passengers, plus crew...you're looking at 30 cases of MREs. Think you can make them share? Better you than me!