I'm not the one saying guns "should" fire faster. "Should" because why? Because a number's in a table? What's better about that number over that number plus the random refire wait? This has nothing to do with gameplay versus fluff, it's that someone picked an arbitrary number and said it's better than the number observed in-game.
Saying that flak turrets should have no random refire delay is on par with saying that BGreens should have a fire wait of 10s.
EDIT: I just realized I have no idea whether TrashMan was directing that at me or Battuta.
Because gameplay/balance/difficulty changes take second place over setting. (and it is directed at everyone)
You notice the AI, damage done and RoF can change with different difficutly setting. So which is canon?
Why should a weapon have a slower rate of fire if mounted on a ship? What possible sensible reason can there be? There isn't one. There is only balance/gameplay. And that reason doesn't exist in the setting.
I say this because it's self-evident. When someone wants to create a mod or a game, first he has to have an idea. He thinks of various ship, races, weapons..things to populate the world with. The setting exist in the creators head before it becomes a game. And when transitioning from one form (media) to another, changes must be made.
Say a dev had the idea of outfitting a Orion with rapid-fire turrets (look at the into cutscene to FS2 and look at how fast the Orions turrets fire). But, after implementing it like that and testing, it was found out that that made the game too difficult for your average gamer. And the game needs to sell. So, you have to make a change from your initial vision to fit the new format. And this format change affects everything. From how durable capships are to damage, rate of fire, etc..
Hence, the original idea - the setting itself - differs from the gameplay out of necessity to make the game fun and playable. However, cutscenes and background fluff do not fall to that restriction. Which is why in games there can be such difference between cutscenes and background descriptions of things and how these things actually feel in the game.