The only logic is that an employee who has been on leave without pay should not get a single rupee benefit from the employer more than what an employee who has worked for the entire month should get.
let us take another example, that, the gross salary (or Basic and DA part only) is Rs 1,20000. His PF contributing salary is Rs 15000. This employee has worked just for 4 days in a month. naturally, his salary for that month would be Rs 16000. Should the employer contribute Rs 1800 towards PF? Shouldn't it be unfair that he contributes the same amount as he does for an employee whose salary is Rs 15000 but has worked for the entire 30 days?
Now coming to the number of days in the ECR, is it 4 days or 30 days that you will put for this employee? When there are 26 days' NCPs, how can you show Rs 15000 as Pensionable salary? Obviously, in respect of this employee the pensional service will be more even though he has worked for very very lesser number of days. Is this right?
It is okay that if the contribution is on actual salary you can show the actual salary (Rs 16000 in this example or Rs 13600 in your previous example) under the PF. Still you cannot put Rs 15000 as Pension salary because the pension salary for 4 days cannot be Rs 15000 but Rs 2000. Then only the non contributory days would get established in his service. If the pension is based on pensionable service and if the pensionable service is based on days worked, you cannot have Rs 15000 as salary in respect of an employee whose salary is higher and even after the deduction for being absent his salary exceeds Rs 15000.
The similar kind of working is adopted in calculating bonus payable in respect fo employee whose bonus qualifying salary is more than Rs 7000. In such cases we calculate bonus assuming that the salary is Rs 7000 or the notified minimum wages whichever is higher, right? In such case, the LOPs shall be deducted from 7000 or the notified wages. The Act has permitted such proportionate deduction also. By this an employee who has taken leave without pay would be getting lesser amount of bonus than an employee who has not taken any leave without pay even if the gross salary of the former is higher than the latter. This can also be illustrated with an example.
The bonus qualifying salary of two employees, A and B, are the same, ie, Rs 12000. (being the statutory minimum wages). Their actual Basic and DA part of salary is Rs 20000. Since they come under the "7000 or minimum wages fixed brackets of the bonus qualifying salary, we can take Rs 12000 and their base for calculation of Bonus. Supposing that the company is declaring a bonus of 8.33%. Then the annual bonus to someone whose monthly salary is Rs 12000 would be roughly Rs 12000. Suppose that A has had 10 days' leave without pay during the financial year ( for which bonus is being calculated). Then the bonus should be calculated on an earning calculated on the basis of a salary after deducting the LOP proportionately from the base amount. That is if 12000 is the monthly salary, it would be Rs 1,44000 for the year. The daily average of 12000 is equal to Rs 400. if the salary were Rs 12000 the employee would have subjected to a deduction of Rs 400 each if he had taken leave without pay. Then for 10 days it would be Rs 4000. Then the annual Bonus qualifying salary would be Rs 1,40000 and the bonus @ 8.33% would be Rs 11,662 whereas for B who has not taken any LOP it would be Rs 12000.