Council rates are levied per household. Obviously you must have separate water meters for the house and the grannyflat. At least two toilets too, so double sewerage, and two rubbish bins so double garbage fees as well.
Being only one title and one ULV, I would imagine that could be negotiable with council with apportioning between the house and the granny flat. I don't think there should be a doubling up on the one ULV, apportioning would be fairer.