Ok fellas, I finally decided to tackle this issue myself. It is SUPER easy.
You need a T45 star bit. I bought a set from Harbor Freight for 24 bucks. Then you need an impact wrench. I am using a 18v Ridgid from Home Depot, but any impact will do. You just need something that will easily break the bolts loose.
I was originally thinking this "whacking" of the latch was to bend something. Not at all. I took the latch completely off just so I could see what the bolts screw in to. Turns out, the nuts on the inside of the body are affixed in such a way that they float. With the bolts about 3/4 of the way turned in, or 1/4 of the way out...both bolts, I put a piece of wood up against them and gave them a light tap. I could then see those backer nuts move a little. I continued to tap them until I got them moved a few mm more inward toward the cab. Lots of folks are suggesting the dealer is "whacking" the latch. You could do this, but then you can't really see the backer nuts move and you are just guessing at how far things are shifting. You could just loosen the bolts and take a few whacks on the latch, but you can't really tell if it's moving. By removing the latch first and then just tapping the bolts, you can clearly and visibly see just how far those nuts are moving inward and not over/under do it.
Pulled out the bolts, reinstall the latch, tightened it all back down and the door now closes tighter and farther into the cab and removed all of the misalignment.
So, for those of you that aren't completely dependent on dealers to fix everything and have some tools laying around to do the job, this is a simple 5 minute fix you can do yourself. Nothing is getting bent and nothing is getting excessively whacked with a hammer. I literally just barely tapped and things shifted right to where they needed to be. For everyone else that likes to argue that they shouldn't have to work on their own vehicles out of principle or spite or whatever....then you guys can just keep waiting on your dealers and/or live with the misalignments. I prefer to take the bull by the horns and just knock these little things out.
I can only attest to this fixing my particular issue where my drivers side rear door was sticking out at the bottom. Obviously having the door shut further into the cab is a logical and obvious solution. Any other misalignments may not be resolved with this method and your mileage may vary.