You can modify and reflash it. I've read all of them. One thing I haven't tried is to install a pig tailed OBD port. So that I have two. My guess is that the BM & MM have a security feature built in that returns to stock when they are unplugged. But I didn't really care to test that far.
However, with the xrt. its designed to be loaded and unplugged like the smarty. So you can read the files, change em, and reflash em.
I want to caution anybody trying this though. There's what 3000 lines of code in the 6.7 ECM. EFi only allows you access to (I haven't actually counted, so just guessing) 150 ish?? Maybe.. Somewhere in there. Regardless, there's lots of other area's that get changed that EFI doesn't give you access to. So if you read out an xrt file, modify it and reflash it. Be prepared for differnt results than what you expect.
Best thing to do is start from your stock file. Modify that to what you want. leave the box tuners crap alone. What we can see looks scary to me. The last xrt file I read had 39.2 deg's of timing built into it. And a lot of pulse. Don't see how any stock truck could keep up with that much pulse width.
Just read out your stock file and start with a clean slate. In my oppinion its easier that way. You don't have the possiblity of little gremlins in the tuning that you can't see.