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Yes, the bottom sticks out so that rain stays outside the channel. I've installed several of these on my vehicles, and family's vehicles. (Weathertech brand, but still in-channel).
No noticeable noise increase, and I've been using them for 18+ years on various vehicles.
The channel seal does come out a little bit at the top, since there's a piece of plastic in there now, but it will seal up tight when the window is closed.