Run as Agent's User works for both Windows and Unix agents and is runs the job as the user that the agent is running on, on that system.  On Windows you can also change the user running the skybot agent service and when a job is run on that agent it will run as the user on the agent service. 

On a Unix system that would typically be the default user which is the skybot user.  On Windows it is the local system account which is the administrator of the system.

When upgrading to 3.0 on the agent there is a setting:  Allow jobs to Run as the Agent's User, this will default to NO.

If a new agent connects on 3.0 or higher the setting:  Allow jobs to Run as the Agent's User will be set to YES.

This feature can be locked down per agent.