You’re not thinking about replicator/transporter technology as broadly as it’s capable of. There could be hundreds of versions of each individual dish. In fact there could be variation algorithms that make it seem like a unique preparation every single time. And people could simply ask for how they want it prepared, like “roasted peppers, spicy” in the same way they ask for “earl gray, hot”.

Even further, transporter technology is the most over powered technology in the whole start trek universe. It’s a thread you can’t start pulling at otherwise the whole fictional universe falls apart.

For example you could kill anyone anywhere without a trace just by transporting a dose of cyanide into their blood. There would be no hallways wasting valuable space inside the ship, people would simply be transported to wherever they wanted to go (aside from a network of small tunnels for emergencies if the transporter is down). And there would be no need for more than a single docking bay at most, just make the entire hull a single sealed surface and transport the entire shuttle and it’s contents inside. Possibly most universe-breaking is that you’d be able to replicate anything, even equipment. Instead of just one enterprise you could replicate it and have a thousand enterprises, or a million enterprises!

I would guess that the writers have imposed some weird limitations on the tech that would prevent these types of scenarios, but i can’t imagine any that could validly apply to what we’ve seen transporters do in all the various episodes.