Generally everything you need in order to develop (town planning, building permit documentation etc) occurs before you have your construction loan approved. This then means you need to pay for this in cash rather than rolled into the loan.
With water fees and all other authority charges some builders will include this in your building contract ie make an allowance for it as Myf has stated.
If you are very lucky you can get construction loan before you go to council - I got the land loan and the construction loan at the beginning - pricing for the construction loan was done off preliminary drawings. They have changed somewhat during the town planning/building permit stage but the price didn't change much so no loan variation was needed.
As such Gwelup includes everything in it But I have 2 properties providing equity for it so the LVR is good.