The Pirates! In an Adventure with Scientists!/WMG

The book, and possibly the film, are set After the End.
This would explain the blatant use of Anachronism Stew (it's all left over from the previous civilization) and why the historical characters are so heavily fictionalized (they're not the originals).

The second film (if there ends up being one) will have Napoleon Bonaparte as the Big Bad, and our heroes will have to save all of Europe from his wrath.
I could see Aardman going in this direction should they get to do a sequel. Napoleon was a character in the fourth book, which gives them a source to draw from. Historical accuracy isn't a problem because it isn't a factor. Having a Take Over the World villain as opposed to another pirate-hating one would raise the stakes and offer more opportunities for action. And don't you just know there would be all kinds of Take That moments and Cheese Eating Surrender Monkeys jokes in it? Plus, Peter Lord has said that Napoleon will make a minor appearance in Adventure With Scientists/Band of Misfits, so putting him in a sequel would be even less of a stretch.

The Pirate With a Scarf really is a woman.
She's just much better at hiding it than the Surprisingly Curvaceous Pirate.
 * And cue the application of Rule 63!

The pirates already know that Surprisingly Curvaceous Pirate is a woman.
But they're all too polite to tell her what a terrible Sweet Polly Oliver she is.

The Surprisingly Curvaceous Pirate is transgender rather than a Sweet Polly Oliver.
There's no evidence that the Pirates! would exclude a woman from their number -- heck, they've even accepted a fish dressed up in a hat -- and at least one example (Cutlass Liz) of a female pirate who's won the respect of her peers. Therefore, Surprisingly Curvaceous has no actual reason for concealing gender apart from her/his own personal preference.

Because Rule of Funny dictates that