Since the specific provision is in respect of "running and maintenance charges" which specifically includes the "chauffeur's remuneration", the amount must be considered in the perqs. When the chauffeur's remuneration is included in the running and maintenance charges, it becomes a part of running and maintenance charges.
Further, the phrase used in the sub-rule is-
"Subject to the provisions of clause (B) of this sub-rule, the actual amount of expenditure incurred by the employer as reduced by the amount specified in Sl. No. (1)(c)(i) above."
If the employer is paying the remuneration to the driver/chauffeur then this is definitely the expenditure incurred by the employer. The sub rule has not used any phrase other than the expenditure incurred by the employer. Nor did it made any distinction between running and maintenance charges or chauffeur remuneration. Since chauffeur remuneration is an expenditure incurred by the employer the same is to be considered for the purpose of the computation of the perquisite u/ Rule 3.