I got my top replaced under warranty this week due to the burrs on the passenger side wearing through.. when I got it home I've been trying to make sure I don't have any issues. I put it through a hose test and was not able to find any issues.. however, we recently had a rain storm and I took myself out and sat in the car for a while to make sure.

What I found was what appears to be a leak into the car, but I wasn't sure if this was the intended method of draining for the vehicle. Directly where the top meets the vehicle behind the seats, the top has a bit of slack.. in this area there is a slight bit of water that gets into the car where the 'brushes' are at that the metal mechanism goes into the car. Is this where some water is intended to be channeled into and then down out the bottom somewhere?

I took a few pics and can host if nobody already has an answer.. thanks!

 

I think that you can expect water to run into the car here at the brushes, because yes below the brushes are drain pipe/holes. As long as not getting into car and on carpet behind seats you should be ok. A wet soft top once dropped will tend to have a wet spot in this area, even after a couple of days. Its best not to drop the roof until has completely dried off.
hope this helps.