Precisely. Airbus SOPs are only guidelines and not instructions. Each company formulates it's own, generally mirroring the manufacturer's but adding it's own fleet-wide practices along the way also. Infact my reference is 3.03.16 Pg4 and not Pg 2 (as is yours) and was revised in July 2003, Rev 36.
It clearly states:
<<<Flaps 3 is required in certain abnormal (system failure) situations. In this case the flight crew shall NOT select Conf 3 on the PERF APP page, in order to keep the VLS CONF FULL value displayed on the MCDU.>>>
Whether the change (absence of) was an oversight of my company (and others in this very thread), or else it prefers the old reasoning I don't exactly know.