Truck Covers USA question

So I have the truck cover usa tonneau cover and I LOVE it. Only thing is it seems like the guys at truck covers got lazy on redesigning the rear handle for the toyota tacoma. See the tailgate of the tacoma sits lower than the bed. So truck covers usa decided to attach a hard foam tube to seal the tailgate. It doesnt look great but it surprisingly protects the inside pretty well from rain. My only thing problem is security and cosmetics. I think someone, if they wanted to could jam a crowbar in there and do work. And cosmetically, well.. it would be nicer if it extended down the tailgate. My question is has anyone ever modified or came up with a solution for this?

 

Can you please tell me where you drilled the drain wholes front and back?