The way to look at this is to consider the PayFast account as a second business bank account and payouts are just a transfer of funds from one account (the PayFast one) to another account (your bank one). This means that all you need to recon is to ensure that the payouts requested from the PayFast account match the payments received to the bank account.
Then to recon each individual transaction, this is done against your shopping system and matched to each order that was processed.
Together these two steps ensure that all funds are accounted for and reconciled.
The running balance on the PayFast account provides additional confirmation that all funds are accounted for.
We do not directly match individual transactions on our side to each payout so it is not likely to match very often. There are more considerations than just the timing and retained balance amounts and we allow payouts for any chosen amount so there is no direct link from transaction to payout.