To Abcesso's credit, they spend some time on the FAQ section of their website defending both ethanol and the AutoFFV. They claim that neither the fuel nor the product will do any damage to your car. They also visit the ol' cold start problem and say that the system software taps the temperature sensor and adjusts accordingly, so no issues should arise. As for the dashboard warning light problem they say that the "'check engine light' in Dodge/Chrysler vehicle will not occur with the AutoFFV system." Not sure why they don't mention Ford, as it's their flex-fuel cars which are currently under the magnifying glass of the NHTSA and FTC.
In any case, from what I can tell, very little has been done to address the use of ethanol blends as high as E85 in modern engines that weren't designed for them. Most reports I found discuss the benefits and safety of E10 while disregarding any blend much higher. Perhaps, we'll have to wait and see.