In my considered opinion, C.T.C. is just an accounting tool that assists in facilitating negotiation in wage/salary determination of employees. As such, it cannot override the statutory provisions of any Labor Law or the Indian Contract Act, 1872.
All the expenses, as well as perks, the value of which can be computed in terms of money, whether they are statutory or otherwise, incurred by the employer to keep an employee under his employment, would form the C.T.C. per annum from the employer's accounting perspective. In other words, it is the total annual cost of employment per employee. Thus, there is a distinction between the monthly salary comprising different components actually payable to the employee and the annual total cost of his employment in which the monthly salary stands subsumed.
If there is a shared understanding of this difference on the part of both the employer and the employee, the question of "deduction from" or "addition to" C.T.C. would not arise in respect of certain benefits, whether statutory or contractual.