If the salary is above Rs. 15,000/-, there's no compulsion that employees should be subjected to EPF subscription, and hence their 'take-home (net) salary' could be higher. I strongly advocate that everyone should contribute to the EPF account, which is also tagged to EPS irrespective of whether or not it exceeds Rs. 15k. Also, the purpose of withdrawing HRA won't be necessary. I would request you to go through the recent judgment of the SC dated 28.2.2019, which has clarified what components of salary would account for EPF recovery (please see the attached document). Considering this, camouflaging in any name of allowance might not work.
Similarly, I would ask you to keep the pattern of salary as it is because HRA is an important aspect of the salary structure, and therefore any decision taken to remove this might pose problems when the taxable income of employees exceeds the limit in the future, affecting the tax planning of employees. If necessary, you may consider reducing the HRA percentage to 30% or so and also adjust the conveyance allowance, which has now been subsumed in 'Standard Deduction' reintroduced for 2018-19 and 19-20.
How about Mediclaim, Accident/Life Insurance policies, and pension contributions?
These assume greater importance nowadays. These are social benefit measures essential in times of need, though they might not directly impact the 'take-home pay.'
Thank you.