E85 will destroy rubber seals and rubber lines if they are of the wrong type.
A flex fuel vehicle would have a fuel pump that has seals that will not degrade as a result of ethanol as well as injector seals and fuel lines safe for use with ethanol.
It should also have tuning that makes AFR and timing accommodations for the different fuel and hopefully different programming for the fuel efficiency calculator. E85 burns cleaner but not as hot. It contains less energy but is significantly more stable so much more timing can be run. Your MPG on e85 is much lower.
The PCM program should take all of that into account.