AUTOTUNE_AXES is a bitmask. On a Heli, you add up the following values:
1 for roll
2 for pitch
4 for yaw
That is, if you want to tune both roll and pitch in a single flight, you add 1 and 2, which makes 3.
In your screenshot, there are two flights, the first wants both roll and pitch to be tuned (hence 3), the second wants to only re-tune pitch (hence 2).
There is a thin line after AUTOTUNE_SEQ for Flight 1 on your screenshot. The next AUTOTUNE_AXES is for Flight 2. Here are the partitions, where I enhance the existing horizontal lines in red color: