http://mathworld.wolfram.com/images/eps-gif/RadicalCircle_1000.gif
I can't edit my posts, so if I can't make the image come through, click the link.
Say a ship's replicator wanted to replicate this molecular pattern: C1, C2, C3- because C1->C2, C1->C3, C3->C1 are three vital compounds a human body needs. Its microscopic, we can't see it. A transporter can make the pattern exactly, using R to bind it like in real food.
Replicators aren't sophisticated enough to to R. If you get a advanced science model, sometimes R, but C1,C2,C3 aren't gonna come out linked enough timed per given area/picoliter to matter for many processes. Remember, everything is being jammed together seemingly at once, at least as nearly instantly, human eyes just see a bit of transparent blurring.
Some replicators might excel at C1->R->C2 bindings, but for whatever absurd reason can't get a whole set that makes your mango taste just right when you bite into it, and it gushes.
One scientist might have a replicator that does a aspect really good C1-C2, while another does C2-C3, while a entire other does C1-C3.
A restaurant reliant on replicated and naturally grown foods might say "we need to use these spices, can't be easily bought, only one kind of replicator makes these spices/fruits right. We only have limited kitchen space, can't have a bulky replicator doing everything, have to be selective".
Could very well be that Captain Sisko's dad used replicator foods in parts of his dishes. Would you insist on harvested salt if a replicator could make that ingredient exactingly? Unlikely.
I'm sure a lot of markets existed for stuff that couldn't be replicated, or required a odd replicator most wouldn't need. Deep Space Nine likely didn't have the best human made food, some foods undoubtedly tasted better on the Defiant. I suspect overwhelmingly most tasted identically. Federation is unlikely to hold replicator codes and mods secret between other worlds who had near ewuivelent tech.
Now, could captain archer's protein synthesizer do things a DS9 replicator couldn't? Quite possibly, I don't think it was a transporter based tech, likely grew proteins through simulated natural processes. Might still have some essential medical applications in later eras. I really don't know. You can today eat (absurdly expensive) petri grown beef patties, it has a similar role as a food replicator for when we get hungry- but a beef vat creates life, replicator merely simulates the form, and that form isn't always exact, very unlikely to qualify as life. Petri dish beef is alive. A later technology isn't necessarily built on a earlier one when trying to fulfill a need, nor does that earlier technology necessarily die off. Like Ibn Khaldun the medieval philosopher noted, sometimes civilizations preserve older crafts and they survive in skillset for a time after the main industry dies off, vistigial, because people already possess that complex skill set and haven't quite lost it yet, due to pride or new use for it.
Older ways, some still futuristic to us, of making food, such as Hibachi cooking, or computer made food like that Carl Jr. machine from Idiocracy, still may exist.
Intact, hibachi chefs in the future might need unique kinds of replicator meats artificially created just to cook right on a grill after being replicated. I'm not sure if you can just toss a uncooked steak into a replicator, replicate it, grill it, and have a good looking, tasty steak. Might not behave like a steak should when cooked- but I'm sure chefs would of noted this, focused on work arounds. The culture of distrusting or disliking replicator food likely comes from early commercial flops in people trying such things. We know dehydrated potato flakes don't taste the same as fresh mashed potatoes made from scratch.
I've done a absurd amount of research in printing stuff over the years. I can't answer stuff on lasers, but printing stuff in general I'm interested. My two posts here aren't canon at all, but doubt anyone has thought about it as in depth as I have here on this site. I'm that boring of a person.