Your question is a little bit confusing. I will try to reply to it in a simple way.
Understanding the Minimum Wages Act
First of all, the Minimum Wages Act only talks about the MINIMUM WAGES + DA. There is no mention of any type of allowances as such. In a few states, there are obligations with certain conditions. For example, in Maharashtra under the Shop & Establishment Act, 10% HRA is applicable if there are more than 50 employees.
Current Practices in Salary Structuring
Nowadays, most companies are paying wages/salaries higher than the Minimum Wages + DA. To save costs for the company while FFS, the excess portion of the said salary is usually bifurcated under different heads of allowances. Similarly, it is also taken care of for the employees when structuring allowances so that they can benefit from Income Tax benefits like HRA, Conveyance, Medical reimbursement, etc. However, by doing so, companies often face TDS problems (which can be very tedious) due to non-compliance of required documents from employees for their tax savings.
Company's Approach to Employee Costs
In such circumstances, the company (which you mentioned in your post) might be willing to incur more costs on employees FFS, i.e., gratuity, leave encashment, than dealing with these problems. As far as the authorities are concerned, when the company pays gross/lump sum salaries "As per or More than MW + DA," they do not have objections.
Normally, such HR policies are framed by the management in mutual understanding with employees. I hope you are satisfied with this reply.
Regards,
Pramod Thakar
[Phone Number Removed For Privacy Reasons], Pune