The guideline requires not to debit the account after it becomes zero. If I had to guess I feel the reasoning behind it would be based on accounting.
Imagine a Savings account not maintaining minimum balance and hence getting debited Rs XX every month. After it becomes zero if it is made negative it essentially makes the liability side of the bank's balance sheet lower, although the said charges may never be recovered. Having multiple such accounts will have a serious impact on the balance sheet (will reduce the liability of the bank)
Just maintaining a record of such charges and debiting then if and when there are funds does not violate the said guidelines.
RBI/2014-15/308
DBR.Dir.BC.No.47/13.03.00/2014-15 point (vi) prevents the account balance to be turned negative. It does not stop the bank from recovering the charges once there is enough balance.
A similar approach prevents the bank from charging interest in a NPA account. Coz that would increase the asset side of the balance sheet with interest that would probably never be serviced. Hence banks do not charge interest to the account but maintain a record of unrealised interest that would be charged if the account holder wishes to closed the account voluntarily or as a result of recovery actions.
