For credit card accounts, the Account Reconciliation task currently compares Statement balance against Balance @ EOM, which triggers a yellow variance flag whenever the card's statement closing date falls before month-end---which is almost always the case.
Could you add an option to compare Statement balance against the QBO ledger balance as of the statement closing date instead? That's the balance the reconciliation actually ties to, so it would clear the false variance flag and eliminate the need to add explanatory notes on every mid-month-close credit card.