I paid $99 Canadian installed at an auto glass place, a big chain. It was just a pop up. It was on my Suzuki Forsa and it was in 1987. Never experienced any leak or rust for the time I owned it, which was another 2 years. The design didn't really need any drainage. This one and I would guess just about any aftermerket pop up has a wide flange/frame that sits on the roof, and is sealed there so no water can creep under. The only place water can get caught is the narrow shallow groove around the glass in the rubber weatherstrip that forms the seal as the glass presses against it. Not enough water to be a concern, and if it does pool in anything it's the frame which is anodized aluminium. You can buy these things pretty cheap and they are easy to install yourself.
Factory sunroofs usually involve the use of a completely different roof panel used in the making of the body, that has the hole with the steel forming a tub like shape around the opening. This allows the glass to be flush without any extra frame stuff, so it looks real slick. I can see how water could collect there and it can definitely rust, so they always have drain lines. My Lumina has 4 of them.
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