You should always verify the allowances in your lot contract for fill, clearing, permits, impact fees and site prep. A good builder will make sure to inspect your lot PRIOR to the execution of your contract to ensure that the allowances for your site specific prep costs are aligned with what is needed. It is still possible to have overages above the adjusted allowances if there are unforeseen circumstances like rock or additional fill, but for the most part doing an inspection in the beginning will eliminate any surprises in the end.