You should not be charged for multiple work. A clutch rebuild on it's own may take a certain amount of time and cost that much. However, that includes disassembly to get to it, the work, and reassembly. Since you are doing a number of other things in that area which will already have the tranny apart, it should reduce that amount considerably. They should only charge you in hours, not for a standard clutch job. That would be simply unnacceptable and if they try, don't stand for it.
You can't get charged for hours of labor that did not occur.