The documentation is not really clear about the differences between the 2 modes (other than the fact that an autonomous program is enabled through a hardware button on the robot), but I guess I understand it now:

Autonomous Mode: Started by the hardware button. Can be executed even if there is no app connected to the robot (phone/tablet/desktop). You can literally turn the robot on and as soon as it finishes booting, start the autonomous program with the hardware button.
Skills: Needs an app to be connected to be executed.

Other than that, you can run any programs either as skills or autonomous programs. There is at least one caveat: You can not fire in autonomous mode (I have no idea why).

Another thing that I did not test yet so I am not sure how it works: It is conceivable that autonomous mode would be disabled when doing battles. I will check later today when I am back at home.

The documentation is not really clear about the differences between the 2 modes (other than the fact that an autonomous program is enabled through a hardware button on the robot), but I guess I understand it now:

Autonomous Mode: Started by the hardware button. Can be executed even if there is no app connected to the robot (phone/tablet/desktop). You can literally turn the robot on and as soon as it finishes booting, start the autonomous program with the hardware button.
Skills: Needs an app to be connected to be executed.

Other than that, you can run any programs either as skills or autonomous programs. There is at least one caveat: You can not fire in autonomous mode (I have no idea why).

Another thing that I did not test yet so I am not sure how it works: It is conceivable that autonomous mode would be disabled when doing battles. I will check later today when I am back at home.