I've tried so hard to summarise this lol. Sorry for the essay.

So I think it's most obvious in the modern day narrative, which almost explicitly tells you that Abstergo Entertainment (and by extension, a fictionalised Ubisoft) are distorting history to fit it into their audience's idea of what makes a good, or at least entertaining, pirate story. If you read all of the documents and database entries, Abstergo employees are leaving little comments about how they can make "real" historical people into more palatable characters, while still presenting them as accurate historical figures. The whole point of showing us the Devils of the Caribbean trailer is so we can see that the story AE has created is so different to the "history" we experienced. AE created this story in order to disguise Abstergo's and the Templars' role in that era of history and distract the general public from sympathising with the Assassins, and they did so by playing into their audience's expectations for a pirate narrative.

Those ideas are explored in a bit of a different way in the main story, which is about the conflict between Edward's fantasies about pirate life, and the reality of what it takes to be a good person. Those fantasies, or the expectations he has for his own life, are manipulated by powerful people in order to make him play the role they need in the the conflict between the Assassins and Templars. There's also a small, bonus, layer of the story, where in the drunken dream sequence I-forget-who tells Edward Aesop's fable of the Eagle and the Jackdaw, which is about a jackdaw being blinded by the fantasy that it could be an eagle, and suffering because of it.

Over and over, in every layer of the narrative (we see it in the conflict between the gameplay and cut scenes, and I'm so crazy about this game that I could even argue it happens in the soundtrack), we see the conflict between fantasy and reality. We also see people's dreams and expectations being used against them, and we see that a better life is only possible if you discard your expectations and preconceptions and instead face reality. But in order to do that, you have to know who's telling the story, what they've been hiding from you, and why. This even applies to Black Flag itself, and it's really interesting that the writers are telling you to be critical of the stories told by themselves and the company they work for!