Allowance of amt of tax in belated return if disallowed in tax audit report because of non payment

Yes pay the VAT return amount before 31.5.21 and file a belated return before that

Filing of belated return under sub-section (4) and revised return under sub-section (5) of Section 139 of the Income-tax Act,1961 for Assessment Year 2020-21, which was required to be filed on or before 31stMarch 2021, may be filed on or before 31stMay 2021.

but under the act you should pay on or before the due date of filing of return of income u/s 139(1).

that is they have extended due dates u/s 139(4),(5) not 139(1).

so if you pay tax now you can take deduction in this for this that is you can claim deduction in coming assessment year.

Ramaraju is right.
you cannot claim vat expense in belated return. you will have to disallow vat expense in belated return as well.
so think before you pay the dues.