I'm not even really sure it's implied in any meaningful way. The rule is that your daemon is of the opposite sex. There are a few unexplained exceptions to that, but nothing to categorically state why it happens.
The movie bothered me for the same reasons the movie version of Harry Potter 5 bothered me. They both neglected real character driven action in an effort to frantically hit all the exciting scenes from the book. It's not helped by the fact that this story got dumbed down an enormous amount from the book and that the world mythology (i.e. the rules governing the fantasy) is so complex. I liked seeing it and I'd like to see the other two, but I don't think it's very realistic to think they'll be made. It doesn't seem like this one is putting up the kind of numbers they'd need it to in order to finance the sequels.
Which says nothing for the fact that the controversial elements related to religion and the church play much more prominently into the Subtle Knife and the Amber Spyglass. I'm not sure how they'd get financing to make the stories without removing them but I'm not sure how they stories would work without leaving them in. Who knows.
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