Here's how I understand the issue:
The new ECM does not permit downloading the factory programming from the OBDII port.
EFILive works by downloading the stock file, you modify, then upload the new file.
Handheld tuners do not download the whole ECM. They get enough info to determine what the addresses are for the tables they want to change. So if the handheld has the addresses for various operating systems, and stores an image of the what was is the target tables on a stock truck, it doesn't need to download the ECM content.
IMO, the real answer will be then generation of harness boxes. Think more of a second ECM than something like an Edge box. It intercepts all the factory data, and uses it as input data, but the real programming will be by the user. They will edit their harness box like EFILive edits the ECM. The harness box will go between the ECM and engine harness, not the bale connectors. This way you can "lie" to the ECM to make it see what you want it to see. This means no speed limiter, no limp tables, no CEL's, unless you program them in yourself. You'll be able to make your own trouble codes if you wish, and datalog things that ECM doesn't support.
This will be far more powerful than anything available to date. The ECM can't limit anything, since it's commands are all intercepted.