Out of these three, labor welfare fund contribution seems to be a fixed amount and not a percentage of (gross/basic) salary.
Now coming to the question, I would say that ESI and EPF are contributed on the total salary. The salary/wages qualifying for the contribution cannot be confined to the statutory minimum wages alone. When an employer is not expected to pay wages that are below the statutory minimum wages, a contribution below the minimum wages is not at all acceptable. But in respect of employees whose actual salary exceeds the minimum wages, the earned salary should be the base for contribution. After all, The EPF & MP Act does not say that PF is payable on actual salary but it can be restricted to the prescribed percentage of Rs. 15,000. Moreover, HRA is excluded from the scope of wages. Though the HRA excluded should be a component of salary paid as a compensatory allowance, the same is permitted in general. Therefore, if the HRA is the element that makes the wages equal to Rs. 15,000 on the minimum wages, then a contribution on that minimum wages will be permissible. For example, if the minimum wages fixed (basic and DA put together) is Rs. 12,000. If you have Rs. 3,000 as HRA but no other allowance, then the gross salary would be Rs. 15,000. In this case, you can contribute PF on the minimum wages, i.e., Rs. 12,000. But if you have Rs. 2,000 as Conveyance allowance, then you will have to pay PF on Rs. 14,000 (12,000 + 2,000).
For ESI, the two components of salary that can be excluded are conveyance allowance and washing allowance. Washing allowance is excluded only if you have provided uniforms to the employees. If your minimum wages are Rs. 12,000, in order to make your ESI qualifying salary equal to the minimum wages, you should keep the balance of Rs. 9,000 as a conveyance allowance. It is not at all reasonable to say that for an employee whose wages are Rs. 12,000 you pay Rs. 9,000 as conveyance allowance. Therefore, it is not practical to bring the ESI and EPF qualifying salary to the minimum wages notified by the government. Since the minimum wages are almost equal to the threshold limit of wages of PF, i.e., Rs. 15,000, an adjustment for PF is practical.