One of the requirements is that "Your partner needs to be Au when the application is to be decided" so as I understand it, should your partner stay beyond the visitor visa max stay of 90 days, the BVA would take effect. However, if exiting before the max stay, the visitor visa is still in effect.
I am not sure though if the remaining validity of the visitor visa is still counted once the BVA takes effect. Perhaps need to apply for a BV with travel facilities to be able to exit and reenter Au before the decision on the partner visa is handed down should there be a need to do so.
Perhaps there are others who have the same situation and experience.