If this is not specified in the contract, the owner is going to want the lower price and will most likely be entitled to it. Subcontractor charges are probably the least subject to dispute, since the contractor will simply pass through the actual amount paid. The issue with equipment or tool purchase is whether the contractor on future projects can use the items being charged to the project. If the answer is no, then clearly the item should be charged to the project. If, however, the contractor on future projects can use the item, the question becomes how much should be allocated to this particular project.
Labor can be a controversial item.
Not only does a contractor pay his or her employees a wage, hut there are associated costs, such as social security, retirement and medical benefits, vacation, etc., that the contractor must pay. These costs are rightfully attributable to the job. Trying to account for these charges is a very difficult task. It is much easier if the contractor simply states an hourly wage that will be charged for each type of person associated with the project. These hourly rates should approximately cover all your associated costs.