Auto-tune tries to find good settings for your GPU's, and it can be controlled with parameter '--gpu-auto-tune'
Your final results will probably be different every time, that's because auto tune searches for the best settings live, and it's not a predefined value.

Modes:

0: disabled
1: normal
2: fast

By default auto-tune is disabled and set to '0'. You can enable it by setting '--gpu-auto-tune' value to 1 or 2.
Sometimes auto-tune won't return you the best settings, and also sometimes it can happen that it won't apply the auto detected settings, so you need to manually set the --gpu-raw-intensity value it returned.

Every GPU thread can be put into auto-tune mode, so you can combine stuff here, for example run a GPU with 2 threads, and set intensity for one of the threads manually, and leave the second on auto-tune.

Check the examples, to get an idea on how to use it.

After getting the result/s (--gpu-intensity), you should set the parameters manually in the batch file and run the miner, even if it will continue mining after the auto tune process is finished.
It's better to use it only for getting the values and then running the miner in normal mode (not auto tune mode)