Yeah, the accordian boot isn't the problem either. The problem will be in between the boot and the box. Where the port passes through into the cab will have a gap around it. When it rains, the rain can run down the front of the box, onto the port and right into the cab and run off there.
One way could be to fill the gap with expanding foam. I wouldn't do this for a couple of reasons. It would be a big mess for one. When you want to change anything in the future you will have to deal with getting the box out, then cleaning the foam up, then re-applying more foam. Also, I would be worried that the motion of the box slightly shifting would eventually either pull the accordian boot loose or make a leak in the foamed part just big enough for water to get through.