It's not over till......
Ausprop, in that case I would assess the wording of the clause that was inserted carefully. Do they specify who values the stage? If done by the builder and you do get an invoice that you feel is overdone (given that you have some experience in building you must have a general idea of most costings by now) then I don't see why you couldn't ask for written justification of the additional payments sought. In order to do this you must have a reasonable idea of what work is part of what stage (usually written in contract schedule a), so that you ensure you are not paying for something that was part of a PP that you have already paid.
If you haven't recieved any progress payments yet ask for a written explanation of this clause, and the conditions under which it will be used (who, what, when etc).
Most banks would probably request an explanation of this type of clause anyway. If you get extremely worried about it then you could speak to the warranty insurance provider's consumer arm and ask them which schedule takes precedence (shedule a, being the industry advised OR the special condition inserted without explanation at the back), that may provide you with some clear answers. I'm a bit disappointed that with the extra education for builders these days, compared to when we were registered, that simple contract management and communication with clients still proves so difficult for some tradespeople. It shows lack of confidence, haste or inexperience to need to insert these clauses without clear explanation and definition to the client.
They most definitely cannot ask for the final payment before the house has C of O issued (or WA equivalent). Read all your clauses carefully now to ensure that you take full advantage of any ones when necessary especially if the house is drawn out..doesn't look good when they ask for monthly payments for a residential house.