We had handled this scenario by creating creating a new rule named Employer PF and ESI. 

We need to created new register named company contribution and add this register for Employer PF and ESI rules.

This rule should not be under Gross, Basic or Deductions instead create new category named company contribution.

Similarly in payslip also you need to ignore this category.

Hope this solution will solve your problem.

Hello

in the salary rule there is option "Appears on Payslip". If this checkbox is unchecked, then this rules value will not display in payslip.

I hope this will helps you.

To generate Employer contribution PF and ESI

Install the Payroll module and go to the configuration --> Salary Rules and make a rule for employer Employer contribution PF and ESI.

Create a rule for "Employer contribution in PF".