Very common rust area, especially in the north. I too have both sides rusted. I am repairing with new metal. I would keep those passages open to allow the water to flow down the inside of the door channel, because at speed the water is pushed back there and forced out. I dont think you could block that area off completely, it would just force the water to go over the blockage anyways, as the cowl panel just sits on top of that area and cannot block it totally. It will not drain forward till you stop. If you are getting water inside your car, it is because the door seal is not doing its job, which might be weak, split or cracked, or there is an open seam or rust hole that is allowing the water to enter under the dash panel before it runs down the inside of the door jam.
I cannot be absolutely sure, but I think that the factory tar pad was black and any color on top of it is because of repainting, I know thats how mine was.
I agree that what ever you do, sealing the metal is the most important part. Epoxy primer those corners, seamsealer, what ever it takes. Actually sounds like a perfect area for POR-15 or Master Series.
Of course, you could just drive it on sunny days with no rain!
