The difference here is that when you "reboot" you are starting all over from scratch and telling it to forget your configurations. A computer is reset to it's previous state and actually uses it's last known configuration. Your Metaphor is more like reformatting the hard drive and reinstalling windows then going through and resetting all the custom settings and hoping you get it right.
That’s simply not true. All of my settings were retained, as stated above. Literally the only difference was a butter smooth tranny, better throttle response, and a much happier truck (and driver). I think you are making way too much of this. You’re just resetting the KAM. No biggie.