I can't make out any specifics (might be my bad) from the quote you posted, Paulrkiii. But from my testing, even with the external tanks switch(es) turned off, upon AA-refueling the external tanks still get filled before the internal ones.
So either there's no way to prevent them from getting filled first whatsoever, or it's not properly modelled in the sim. That, or I'm making a major donkey of myself here :)