If you only intend to load up an OTS tune and that's it, the main difference is in the AccessPort hardware device, the firmware functions, and the datalogging capability.
All of the Cobb work is done in-house. Trey Cobb, the founder, is an Electrical Engineer and they employ real software engineers. They FULLY evaluate every vehicle they support, reverse engineer the ECU, and write their own software interface and add custom code to implement functions requested by the user community and/or where needed for performance. ALL the other tuners use someone else's software (HP Tuners) and can only do what they're allowed by HPT, which are the basic existing functions in the ECU. (I have the HP Tuners software as well)
If the user is interested in DITY tuning using the Cobb AccessTuner software, then Cobb requires you to complete a course of EFI U training (~$150) that touches on the capabilities and the emissions to be sure that the user understands the basics and that it becomes the user responsibility for emissions compliance. You will get a formal certificate of completion. Once completed, you can order the AT software. The AT software has explanations/notes on each table to help the Pro and DITY tuner understand the function(s). Cobb understands and writes the tuning process from end-to-end, so there are no "middle-men" tuners like MPT, 5-Star, etc. When you have a question, it goes straight to the source of the code, if necessary.
The Cobb OTS maps provided for free with the purchase of the AccessPort also do not "turn off" or defeat emissions devices. They are setup for increased performance at safe levels. If you're looking for maximum performance with more risk, then a Pro-Tune or DITY is required with AT.
There's so much more if you're into the actual tuning, but this is a top-level overview. You can study their web site and even send them questions if you have specifics on vehicles they support, which are listed. They don't support a whole line of vehicles, only the vehicles with potential that they take in-house and work their process on.
I'm beyond ready for them to get done with the Raptor 3.5 and release their product line. I'll be one of the first to purchase the AP, and I'm already Ford Ecoboost certified, so I'll get the AT software too,