The amount payable to the Australian Taxation Office in the BAS return does not match with the actual payment in the bank account due to other tax components. What should I do about the difference in amount due to other tax components?

You can record the payment/claim transaction for the BAS return and match the bank feed with that transaction. As for the difference amount, you can add an adjustment from the matching screen and track the adjustment amount as an expense (if it is a payment) or as an income account (if it is a claim).