It should not cost any more for them to leave in a few ridges or humps as they are taking out dirt. In fact it should save some time and $ to do so. Not to mention how much easier it is for large equipment to drag a couple trees or stumps and put them in. One thing is certain -- it won't cost anything to ask the contractor about that option. The biggest cost is loading and hauling the excess dirt. Good luck with the project. What is the next step after its built?