The only part of the program that matters for the auto tune is the set temp for step 1. That is the temperature the PID will attempt to hold the box at, and auto tune for.
For your example in the original post, it will auto tune for 140F, regardless of how long it takes.
Once auto tune completes, the Auber will run through the program inconsequentially.
Not sure what happens if you engage auto tune mode while the Auber is in the second step of a program; never done it.
That said, the temperature chosen will affect the outcome tuning (PID parameters). Probably best to pick a temp you usually cook at. If you are a 225F man, set step one to 225F.
I usually run a program like this for safety. Set the program, enable auto tune. It will perform the auto tune, then run the set temp for 6 minutes and shutoff.
225F for 0.1hours
0F for 0.0hours (steps 2-6)