I don't know if this issue will every be totally resolved. When I started this thread I was working on a '13 DRW, as I stated everything made it better, but nothing completely fixed it.
Now I have a '16 Megacab SRW. It vibrated when new, but no where near as bad as the '13 originally did. Since then I have added Centramatics wheel balancers which helped. Then in one shot I stretched the frame to make it a longbox and added a complete Kelderman air ride system. In doing so they completely replaced the driveshaft and added a new carrier, so that would replace driveshaft issues, the rear suspension was 100% replaced, not a single stock item remains as the new system is a 4 link setup riding strictly on airbags with new Bilstein shocks, the front end replaces the coils with air bags, but the rest of the suspension remained. As it stands the truck is better than when it was new, considerably better than my '13 was even after the upgrades, but still has a vibration.
I notice the vibration most when driving empty, pulling my 5th wheel I don't notice it much at all. Now before you think driveline angles are changed because of the load, remember I have full air ride which maintains the same ride height no matter how much weight I'm carrying. Maybe it's because the tires themselves are flexing more due to the load and that is absorbing some of the vibration? I just leave my rear tires at 75psi because I'm generally hitched up to something. I lowered them to 45 psi once for a long distance trip empty and did notice an improved ride, but I honestly can't tell you if the vibration was better or not.
I know I can get out of my 1/2 ton and into my 1 ton and drive the exact same stretch of highway back to back and the difference is tremendous. I think I've just become accustomed to the vibration in the one ton but it slaps me in the face when I compare it to my Corvette or 1/2 ton if I'm immediately changing seats.