I think section 206AA contains the words "notwithstanding anything contained in any other provisions of this Act". Hence it has got the overriding effect on section 90 as well..
Further please refer the following case law:
Bosch Limited [TS-904-ITAT-2012(Bangalore)].
Further please refer the following case law:
Bosch Limited [TS-904-ITAT-2012(Bangalore)].