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1) Will the API allow resetting of the integral value? Preferably to an arbitrary value, and not just zero

We are not currently planning on providing such an API, please file a feature request if it's important to your controller development.

2) How will the controller handle saturation?  (will there be integral tie back to prevent windup?)

The effort command produced by the integral term is limited by [i_effort_min, i_effort_max].

3) What are the units of terms? (e.g. N*m, fraction max effort, ...).

We will be using MKS throughout DRCSIM.

4) Related to (2) and (3), will the individual actuator limits be published, or are we responsible for parsing the model definition file?

In ROS, the common practice is to obtain the Robot URDF from the ROS parameter server and use existing libraries to parse it.

5) Will the jointCommands be issued in a vector to guarantee synchronous execution, or will the individual joint commands be sent separately? If latter, is there any way to guarantee coordinated execution?

Each subsystem (Atlas, right hand, left hand and head) is expected to receive JointCommands messages containing commands for all joints simultaneously. We do not expect to coordinate execution between subsystems.