When removed from the vehicle you will still have traces of e85 in the fuel system which is an easy check for the dealer. Oil analysis will also show the use of e85. And a quick look at the PCM will show roughly 30% higher injector duty cycles for a given CFM into the motor in its history. There are actually multiple other threads about this product on this site discussing this about 2 years ago. There is no way to run e85 and keep the factory powertrain warranty. It’s gone.
You are confusing two different topics about the powertrain with regard to modding and tuning. The first is strengthening the drivetrain to handle higher loads. The second is actually adjusting tuning to manage those higher loads. When you tune you don’t “remove the stock limits,” you change the management of hundreds of variables in order to avoid applying increased loads to the drivetrain (especially shock and frictional).
All that commander adjusts is fuel flow based on ethanol content. A proper tune on the PCM/TCM for changes in fuel type will adjust fuel, timing, torque management, shift controls, etc. For a simple example, you are pushing 10% more torque via e85 and the commander through the trans. Constant torque through the drivetrain doesn’t do much damage until you are far exceeding the initial design limit. However, you are also using the entire stock TCM map for that 10% higher torque for shift times, line pressures, torque management, etc which means you are asking the trans to “shift the same” with the increased power. On the actual correct tune you dial these down or up accordingly to minimize wear on the trans and driveline. I have two different TCM maps for my truck. One is low wear on the trans where we have adjusted all of the torque management to minimize driveline shock and eating up the friction plates with longer shift times, FSO, etc. Run this daily and when towing. The other is a faster shifting setup which will wear the trans components more quickly just for the strip.
In other words, a proper tune can be setup to both utilize the power benefit of the e85 and mitigate the added stress on the drivetrain. The commander cannot do both. Personally if I’m out of warranty then I want to mitigate the added stress.
