Well, I can't explain why GM do any of what they do. I mean why would they 'really' need to have released over 25 operating systems for the E38 in a 2 year period!
I don't know why some tunes seem rougher than others, it does seem odd that they would go from 12.4:1 AFR to 11.02:1 AFR within the space of 1500RPM in the PE table on the LS2 Vette, yet the same year SUV's, trucks seem 'normal'.
I'm sure they have their reasons, I just don't know what they are, but I have a feeling they probably aren't looking at nice 2D/3D graphs like you guys get to.
Cheers,
Ross