I think you guys are giving GM way too much credit. Having looked through a bunch of stock Duramax and LS tunes, I think GM gets it close, then phones it in once it passes emissions and makes their power target. The stock LB7 tune is a hot mess, especially the early ones.
I don't believe this was done to protect the crank. The amount of fuel is way too low to do anything meaningful. Plus, think of the shock loading the moment you step on the throttle after exhaust braking down a hill. It goes from ~0 mm3 to 40+ instantly. That first cylinder will have a huge differential loading vs the rest (which are still at 0).
I have noticed a recurring theme on stock Duramax tunes that might explain this, though. GM has had the timing for low fuel amounts (0-5 mm3) set really high since the beginning, and what this does is cause a "growl" as the transmission downshifts, especially in tow/haul. My dad (and probably lots of others) really, really like this sound on the downshift. I've played with the timing in that range, and the only thing it seems to do is change the note of the growl. I'm guessing GM did something similar on the L5P, and it isn't supposed to happen except in tow/haul.
Not that anyone asked for it, but that's my :2cents: