In addition to what Mr. Madhu has stated, I would like to share my views on the question. In general, wages, salary, remuneration, pay, etc., are synonyms indicating the total sum of payments made by the employer to the employee for the work done over a fixed period as agreed upon in the contract of employment. The connotation may differ according to the status and mode of employment.
Formal Employment and Remuneration Structure
However, when employment becomes formal, regular, and structured, in order to minimize certain indirect commitments of the employer towards fringe benefits like social security, bonus, etc., as suggested by Madhu, the total sum payable is broken into different components such as basic salary, dearness allowance, House Rent Allowance (HRA), conveyance allowance, medical allowance, traveling allowance, and the like.
An employer's progressiveness, generosity, and people-oriented approach can be deduced from the remuneration structure adopted. Unfortunately, the opposite is often true based on the principle of Cost To the Company (CTC).
Special Allowance as a Component of Wages
When it is not possible to classify any portion of the payment, it is termed as a special allowance without any specific relevance to the employment or payment itself. This is how it becomes a component of effective remuneration for the purpose of the employer's statutory financial commitments, as indicated by Madhu.
If I remember correctly, there is a Supreme Court judgment upholding any payment under the nomenclature of Special Allowance as an inseparable component of wages. Therefore, the phrase "any sum paid to the person employed to defray special expenses entailed by the nature of employment" indicates only the direct relationship between the employee's performance of duties and the expenses.