As per Chartered Accountants Act 1949 , there is guidelines which gave basic principles that what CA can do and which act can be against the act and regarded as Professional Misconduct .
As per Companies act there a company can't be auditor so there is no chances of related party transaction or transaction which might have significant influence.
As per your question there is a Firm and an accountant rented his property to the firm . Firm is paying salary as an accountant and rent as well .
Its no where mentioned that accountant is partner or relative of partner of the firm (even in that case answer going to be same) .
Commercial transaction a transaction where two or more party agreed to share goods, service or something which has value in exchange of reward in cash or in kind .Its a kind of contract whether oral or written . These type of transactions are always at Arm's Length Price.
On the above discussion it can be concluded that here there is no direct/indirect relationship between partner and accountant ( so no need to check related party transaction or not to be shown in their report ) so there is no restriction with regard to such type of transaction. Its fully allowable to pay salary along with rent.