I think it's a combination of both reasons you've listed. The gap is there so the bed won't rub up against the cab and the weather strip is just there to hide the large gap while preventing debris from getting inside.
Read a bit a while back that said the strip is also there to reduce air flow and turbulence along the side of the truck, reducing drag and helping mileage a bit. Not sure how true that is, but it does make some sense.
The gap size on the Rebel is identical to the gap that was on my 2015 Tradesman. It's also identical to the gap that is on my girlfriend's Laramie. And all of them have the rubber strip. The gap does seem bigger than the gap that was on any of my previous GM pick-ups. It was large enough that I noticed it right away after I bought the Tradesman and got it home.