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.
I mean, that is conjecture right? With how much the real military puts into food science, I could imagine that there’s a Federation food science division that could easily make a dish from scratch a number of times and store each attempt’s pattern as a random variation that gets distributed out to the fleet.
When I was in, they put zero thought into it other than “needs more calories” and “make soldiers poop less.”
Considering a post-scarcity universe where the machines they’re working with can take even those considerations away from us (IIRC the replicators automatically do adjust nutrients/calories per-person per-meal). I think after a while, someone would’ve just… Gotten bored and futzed with it. I’d also assume consumers on earth to contribute to the databases. Heck, there could be a whole food influencer culture thing going on. “Oh man, you haven’t lived until you’ve tried ‘eggs, scrambled, variant 37578a’!”