Well, the film doesn't really provide clear answers here. All of these are juggled with various levels of success, with the war with Spain taking precedent over the others. However, that means that other issues are skimmed over, and never feel important to the story. The film simply takes on too much for its 112 minute running time: this is a case when a film arguably needs to be longer.
The result of this is that we get a film that's mostly style with very little substance. Kapur doesn't even seem interested in adding layers to the story, aside from some very heavy-handed visual metaphors: for example, Elizabeth tells a Spanish ambassador that she's "got a hurricane in her," and when the Spanish Armada attacks later, a violent storm appears as she stands on a cliff overlooking the fight; so much for subtlety. Kapur wants to show us how exquisitely beautiful and splendid the setpieces and costumes are, which are indeed quite stunning (if historically inaccurate). That highlights the main point for this movie: its a feast for the eyes, with little interest in engaging the brain. It's a true, pure costume drama.
The performances are mostly lacking in substance as well, with Owen and Blanchett carrying most of the weight. Blanchett received a surprising Best Actress Oscar nomination for the role (which she was also nominated for in 1998), but it's not necessarily an undeserving one. She does well at making Elizabeth a complex and likable character that we can emphasize with, but the last half-hour of the film, in which she gets to be a female William Wallace, doesn't seem faithful to the character that had been presented before; she feels contrived to fit the "rah-rah" attitude of defeating the Spanish. Owen, however, does untamed explorer effortlessly, and steals pretty much any scene he's in. It's just another case that he should be a bigger star than he is.
Elizabeth: The Golden Age is an enjoyable visual feast, but don't expect to learn too much about Elizabeth and a critical moment in European history.