Hi mpp,
Boutique initially included a $15k allowance for site costs in our original quote but then once we got the actual costs this went down to just under $13k (including about $2500 in council requirements - so site costs were just under $10k).
We actually got our site costs done before signing our PWC because we wanted to know exactly what we were going to be paying before signing anything - we didn't want to get any nasty shocks with the site costs. So basically our contract doesn't have any allowances, everything that's in the PWC is fixed in the contract. Any upgrades we make at pre-start we'll pay for out of pocket.
Hope that helps!