The builder may be dropping the floor to create a full mortar bed tile installation in the shower area. This mortar takes up more depth than a typical 'thin set" tile installation over a thin cement board. The thicker mortar build up is needed to get the slope to the shower drain. It sounds more than plausible for what might be needed for your installation. I would ask questions and have him explain the process to you. I find that good communication always makes for a better project and more confidence between the parties involved.