Out of interest why is the cost so high for this project? All they really need to do is cordon off one gate lounge and put in a customs screening point in the lounge at departure and have another one in the arrivals hall. In reality the barriers can all be temporary once it's on it's way you're back to domestic.
Adelaide airport is a good example of how it can be done pretty easily.
I have also flown out of airports in the US and Europe where international flights depart from domestic aprons. So whilst it's probably not what Perth Airport want I don't think it's really that big a deal for one flight a day. All they need is a few barriers and customs.