site costs are an interesting topic - each builder has it's own policies. you can choose fixed or just leave it and pay actual costs. I choose to fixed option as one would think that this is the better option and saves any potential future bickering with your builder when presented with an outrageous invoice. I am in Stage 2 and my site costs are at a 11,700 with no Estate Guidelines Cost - actually this is the first I've heard of this and if I was you, I would ask H3nly to point out in your land contract under what clause this is indicated.
Although H3nly might estimate this and then provide a refund once done.............. Builders / Refund just does sound right together
No harm in questioning and asking for supporting evidence