It is explicitly stated in the FCTM Takeoff section:
During certification, maximum manual braking and speedbrakes are used. Thrust reversers are not used. Although reverse thrust and autobrakes are not used in determining the FAR accelerate-stop distance, thrust reversers and RTO autobrakes should be used during any operational rejected takeoff.
So autobrake is not "assumed to be inop", it's just not part of certification. But Boeing (and most likely your operator) recommend you let the Autobrake do its job.
P