The reconciliation problem has three dates
A WooCommerce order can be created on one day, payment captured on another and the processor settlement paid to the bank later. If accounting uses only the bank deposit date, sales timing becomes distorted. If it uses only the order date, the clearing balance may not match captured payments.
Start by separating the payment methods
Do not put every gateway into one generic bucket unless the business deliberately wants that. Stripe, PayPal, other card processors and BACS can be given different Xero accounts or posting behaviour.
Then reconcile each method on its own evidence
The ecommerce summary provides the gross activity. Processor settlements and fees explain movement out of the clearing account. Manual methods can remain unpaid until the bank receipt proves settlement.