If you stop up that hole you'll stop the water being able to drain out from that channel when the roof is up or any that gets under there while the roof is down. Open cell foam might allow water to drain but will get clogged with dust and dirt in the process.
Have you stuffed something in temporarily to see if it makes any difference to the noise levels?
If you block the channel there you'll likely get water running over the door and into the van every time you open the doors when it's raining.
I glued some foam pieces in each channel under where the pop top rubber sits.
I had no problems with water pooling over 3 years.
It really did reduce the wind noise (it’s directly above the front seats) and you could simply wipe the channel before you put the top down…if it’s been raining that is.