The browser is more important than the websites it renders, up to where preferences are concerned. Would you like websites to override your pop-up blocking preferences?
No, but that's a security preference, I don't want the browser overriding well-known Javascript APIs. Here's another example: Firefox for Android uses a swipe to the left to get to your tabs and a swipe to your right to get to favorites/navigation controls. This means that any site that uses swipe gestures for UI are broken. Google+ doesn't work on Firefox for Android for this reason. To me this is browser fail, not website fail.
