Most aircraft if not all are sold through agents. The aircraft may leave the factory as a basic model and without the many options that can be added later by the agent as a buyers option. The POH/Flight/Owners pre-printed manual will provide the data for the basic factory model. The weight and balance report of the modified aeroplane is therefore the overriding document and is inserted within the manual. If the aircraft is sold by the factory as a completed ready to fly aeroplane they will also provide the actual W & B report including the modifications the buyer has stipulated.
I'm not sure from which you quote but I suspect the heads up was issued to remind owners to always refer to the W & B report and not the manual alone.