Nothing in the CTC portion, which is mentioned under the Gross Salary portion, will be actual. Take the case of EPF contribution, which is shown as part of CTC below the Gross salary level. This is the employer's share of the salary mentioned above the line at the time of the offer letter or revision letter, as the case may be. It will vary if the employee takes a few days' leave without pay.
Again, some companies mention gratuity as part of CTC, which is in no way related to the actual figure. What is assumed is that this would be the PF payable by the employer in respect of the employee concerned if he works for all the days and thereby the salary remains the same.
In a similar way, if you show a bonus as part of CTC, it only means that with the salary given (above), he would get the bonus as mentioned. Obviously, if he takes a few days' leave without pay, his salary would be less, and a proportionate reduction will be there in the Bonus also. That is not an issue and cannot be fixed.