If there was a split the the Coalition, then what would happen in the states where the two parties have actually merged?
In 1998 they had only merged in the NT, the Nats never existed in Tassie and in Qld the LNP hadn't happened and presumably won't happen.
The 1999 rerefendum question, in the event of it passing, is signed, sealed and delivered. I don't see what the Coalition government could do to amend it and keep it minimalist (the constitutional amedment is this, after all: To alter the Constitution to establish the Commonwealth of Australia as a republic with the Queen and Governor-General being replaced by a President appointed by a two-thirds majority of the members of the Commonwealth Parliament.)
A President appointed by 2/3rd of the house is a minimalist model, i.e. basically no change, but you are right that the wording of the referendum means that even if Howards gets run over by a bus you aren't going to get a popularly elected President.