What needs to happen is someone to make a piggy-back system for these trucks. Been doing it with EFI motorcycles forever... Bazzaz, Power Commander, etc...
Small box with harnesses to plug inline with the injectors, and if you get the ignition module, the coils as well.
Plugs into a laptop, and you remap the fuel and timing tables as needed, but altering the width of the pulses that the ECM is sending to the injectors... You tune it by throttle position and in 250rpm increments and you can take whatever the ECM is sending to the injectors, and add or remove fuel from that "cell" on the mapping tables. It's easy, doesn't write anything to the ECM that would show up in a dealer scan, etc...
Only thing would be the need to disable any lambda sensors so that the ECM doesn't see the exhaust as "rich" and try to lean it back out and undo your tuning changes... That is usually done with resistors to send a steady signal to the ECM so it doesn't see any changes...
I know many of you know this stuff, but some might not. It's how most motorcycles have been tuned for the past 15 years. For a bike, the box is $350 and us plug and play, and you can download and run canned maps, or take it to a shop with a dyno and the software and have them custom tune your truck.
If you have to to take the truck to the dealer for warranty work, unplug everything and put it back to stock, and then plug it all back in when you get it back home...
I feel like that may be the only real way to tune these trucks going forward...