Dear Thirumurugan,
A definition is ordinarily the crystallisation of a legal concept promoting precision and rounding off of blurred edges. Sometimes a definition extends the ordinary meaning and sometimes it restricts the same. Therefore, a definition clause in any statute does not necessarily apply in all possible contexts in which the defined words may be found therein. Hence the definition clause must be read in the context of the subject-matter and the scheme of the Act and consistently with the objects and other provisions of the Act.
In this back drop, the definition of the term "wages" occurring in the Minimum Wages Act,1948 quoted by you is only for the purpose of fixing minimum rates of wages in certain employments. If you look at the term "wages" as defined u/s 2 (vi) of the Payment of Wages Act,1936, you can find some additional heads of remuneration included in the definition for the purpose of the latter enactment is to ensure that wages actually disbursable to workers covered by the Act are disbursed within the prescribed wage-period and employees get their full wages without any deductions which are not specifically authorised by the Law.
Here the gist of all your queries, if I were correct, is relating to breaking up of the single package of wages into different components and their scales. In other words, it is the bifurcation of the entire package of wages into two major heads viz., Basic wages and allowances. It, therefore, implies that originally wages for the services rendered by the employee meant only the basic wages and allowances came to be added later as a compensatory measure for the purpose of retaining the employee on the job due to reasons of migration of labor and collective bargaining. Hence, whatever be the allowances, they have to be computed relative to the basic or original wages.
As such, a relatively determined component like HRA can not be more than the basic wages just because it forms part of the term "wages" as defined under any law enacted for a different purpose. You also should bear in mind that HRA is not included in the calculation of statutory terminal and social security benefits. Moreover, such move would be viewed as cynical.