Good post LNIDA, that should clarify the nav system operation.
The important point bought out is that there are only two possible scenarios. At the southerly turn point there was either a live operator at the controls to manually select a southerly heading with the heading select control or the FMS had been preprogrammed to make the turn and a live operator was not required.
Either option suggests that the person in control of the aircraft had some training on nav. system operation but it does not imply that a crew member was flying the aircraft. The system is simple enough to operate that a lightly trained hijacker could have steered the aircraft - after all hijackers took flying lessons for 9/11.