The big difference is Standback is a piggy back intercepting the signal and the AP is a flash of the ECU itself. Anyone can tune the AP with ATR, professional or not.
As far as the video - it was fun, but pointless. Every variable of the Cobb AP is tunable with ATR. They used a tune made by Christian with Cobb. Ok - obviously he was more conservative than Laloosh was with the Standback tune. IMO it was not an unbiased apples to apples comparison.
It's in the tune, not the device used to create the tune. I hate the concept of piggy backs but I know they work for many. If there were better custom tuners using one product or the other that would certainly make me consider it

But I'm still running mediocre OTS tunes.
Regarding AMS, they will tune any piggyback and a long list of other products including the AP so you are wrong.
Check the link:
http://www.amsperformance.com/dynotuning.php
Buschur Racing...another EVO tuner (AMS and Buschur are irrelevent to Mazda don't you think?)
They flash the ECU themselves, they aren't using a piggy back like CPE. Really pointless to bring up either of these companies in the discussion.
No offense to CPE, but I don't think they are in the same league as AMS or Buschur.