The Raptor has a PCM and it's post 2010 1/2 and with each newer year the PCM gets bigger and the software gets more complicated, so theres more than just engine tables and like I stated before it's good practice.
It also is the first thing the Ford Hotline Engineers want the techs to preform when you bring in your truck for shift and engine issues. And then they will tell you they reset the computer and send you on your way.
I know there's a lot on this forum that don't do the disconnect, but I also see a lot of guys stating weird things happening, even if you call Mike at 5Star or SCT direct they will suggest doing a battery disconnect.
It's also good practice the have a fully charged battery and make sure nothing is on, disable your alarm so it won't set while your tuning, don't open or close doors, etc....
Now in my case when I change tunes, it was recommended to go back to stock Tune before loading another Whipple Tune.