Two reasons, actually.
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It’s not their preferred preparation. All the replicated food is based on a pattern from an original recipe. It’s not adding flair or anything, it’s literally a copy of a dish made who knows how long ago. And that’s where the next reason comes from:
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Imagine eating some spicy pepper dish from, like, the 1940’s vs the same dish made today with spicer peppers. It wouldn’t be as spicy eating something that wasn’t, at the time, really selectively bred to be more spicy. If the recipe for the replicator is, like, hundreds of years old it would probably not be as potent as the same dish made with real ingredients.
I can imagine that the characters that have expressed disdain for replicated food probably get hit by both of these. It’s not the way they would preferred it to be made, and it’s also like eating vegetable jello salad in 2024.
Yeah, that’s true. Could be that only senior officers can program recipes, or maybe the Cerritos has special rules. They were under heightened security after the Pakled attacks, and also, considering the Buffer Time episode, Captain Freeman is definitely the kind of captain that would make rules about that. And the Cerritos seems like the kind of crew that would need them lol
Welp, that’s my new head canon now. The rules were made after a noodle incident [warning: TVTropes link] involving literal noodles (or maybe gagh).