I have already given many comments on the applicable wages for PF, Gratuity, leave encashment, Bonus, etc. To summarize in a single sentence, the wage considered for deducting the salary of an employee if they have taken LOP is the wage used for deciding PF, Gratuity, or retrenchment allowance or anything else. For example, if your salary is Rs 15,000, of which you have fixed Rs 6,000 as Basic salary and have been deducting PF on this amount only, you similarly use this amount for computing Bonus, leave encashment, and obviously, gratuity. However, if the employee takes leave without pay, you will deduct Rs 500 from their salary, which is one 30th of 15,000. If their salary is Rs 6,000 and all other components are just allowances, why can't you deduct only Rs 200, being one 30th of Rs 6,000?
Basic Salary Definition
Basic Salary means the salary as per the contract of employment. Anything paid in addition to this is an allowance, and only such allowances can be excluded from PF, Gratuity, etc. Obviously, for PF, the employer even has the privilege of restricting it to Rs 15,000. Even HRA is part of the salary if paid to all employees without considering whether they live in a rented house or not. A washing allowance paid to employees to whom you have not provided a uniform is also part of the salary even for calculating ESI.
Restructuring Salary and Employee Impact
Restructuring the salary, keeping the cost-to-company unchanged based on changes in the law, is unfair. If permitted, then poor employees will become victims even when there is a hike in salary by means of a notification from the government. The employer will not hesitate to add the electricity charges of a ceiling fan put for an employee or the tea and snacks the employer provides for the employee to make it equal to the statutory salary. Therefore, I will never give advice on how you can restructure your salary to protect your employer. I will only advise that PF is an investment and whatever deduction the employee may have in their take-home salary is only temporary. Being an HR person, convince the employees that a higher contribution would result in higher PF and a higher pension.