You will not have a soot problem with the new truck (I have a Ford but I'm sure you will have the same experience). These new ones are amazing. No smell. No black smoke. Just nothing. If that's the reason you want to change out the exhaust, then don't waste your money.
The reason Ford warns you about plugging those holes near the exhaust tip is because they suck in outside air to cool the exhaust coming through and out the tips during the regen process. It's super hot. I had to shut mine down the other day part way thru a regen which kicked in while I was running errands around town. I walked back to see just how hot the tailpipe was and was shocked that I could feel blistering temps when I put my hand close to the tip. Touching it would have meant a nice big blister. The holes have nothing to do with back pressure, which they have no effect on.