I've had the Leer Tonneau on for a couple of years now and have hauled boxes (cardboard here) in both pouring rain and snow on the freeway. I've never put the seal around the tailgate because I wanted to see if I ever got water in through the "gaping" gap. Never have, so I've never needed the seal. But, what gets in there a lot is dust when driving on dirt roads! So, put it on/keep it on if you don't want dust in the bed.
One area I had to seal to keep water out is the front corners at the seams where the sides meet the front. There's a gaping hole on each side under the top lip of the bed. Tons of silicone to seal.