I would imagine a lot of companies now use a 3rd party when receiving payments from customers , whilst the customer pays by Afterpay (for example), in full, the amount transferred to us is less their commission which makes it very hard to claim the tax in Reckon Retail Premier.
Reckon Accounts underlying logic does not treat deposits as sales, but as movements of funds from one account to the other eg undeposited funds to bank.
The correct process to deduct fees from a sale, or indeed record a sale, is to use a SALES RECEIPT for example, and directly deposit this to a bank account, deducting fees using a discount item or a negative qty. This will ensure the tax treatment for sales and purchases are correct on your BAS and tax reports.
nb. If your sales receipts go directly to undeposited funds by default, and don't allow the selection of a bank account, you may need to change this preference (un-tick it).