The feature went through several iterations. Originally, popups were just shown with their requested size anywhere within the browser window. The idea was that a page could only damage itself by opening popups and not interfere with your window manager state.
This was deemed ineffective (sites knowingly do stuff to themselves like this all the time - e.g. overlay divs), so we auto-positioned them at the bottom right and hoped you figure out that their titlebars were stacked down there and would drag them up.
Then we made them detach immediately when you clicked them.
Then we got the feedback evmar mentions and we just did the boring thing. Personally I find it less discoverable now (and am constantly missing popups) but non-user-gesture generated popups seem relatively rare on the web these days compared to more annoying stuff.