I have used SCT to tune older Mustangs. There are precanned tunes that you can use from SCT. Example, there are tunes for several MAF or cold air kits that you can choose from, you can choose to run 93 octane fuel, and etc. Also with SCT, a tuner can customize the tune to what ever the tuner wants.
So IMHO if the tuner used the precanned tunes, SCT should take some blame (but they do have warnings that they are not respossible for damage). If the tuner actually tweeked the turn from SCT precanned tunes, then I would think it would be the tuners responsibility.
It is tough when you start modifying from stock. Ford must be having lots of problems to put out a TSB.