Your big question was "Why is this?" Ask Microsoft about that one -- the alert occurs before the window opens, and it's the window that makes the request. (window.open provides the window and passes the href as a parameter, then the new window makes the actual request.)
Is the pop-up necessary? I don't mean to ask "is what the pop-up does necessary", but is the pop-up itself necessary? Pop-up blocking is becoming as big a hobby as checking the "warn me" box, so if you can get around requiring a pop-up, you should be able to kill two birds with one stone, so to speak. If the pop-up content were moved to, say, a high-z-index, normally-invisible <div>, you could get your "pop-up" without opening a new window. How practical that would be depends on the content and purpose of the pop-up.
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. . RE: https > https popup (~Justin Minlute... 19.Jan.04) 
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