Stripe/GoCardless Payment Processor payouts - Accounts reconciliation
The most common approach to reconciliation is to update contributions within the CRM with the identifier from the payment processor. For Stripe we have a few approaches, our most recent is the payout reference from Stripe is automatically pulled back into CiviCRM. This allows the finance departments to run a payout report from both systems and reconcile. This has proved to be a very reliable and streamlined process. With GoCardless it's not possible to do an automated process unless you have the pro version with access to their APIs. You can perform a similar function by updating contributions in CiviCRM using the GoCardless data.

The key to a streamlined process is finance being able to easily find all the transaction which make up the transaction into their bank account, which involves some flow of information back from the payment processor into the CRM. The unfortunate part of this is all of the payment processors have varying levels of APIs and data to access.