I'm from Better Reports and your question piqued my interest. Our app does reporting and some of our customers are exporting those reports to CSV so that they can import their transactions in their accounting software.
Do you use an app to automatically import your orders into Quickbooks?
If so, I suspect that most of these integration apps are not pulling the transaction fee.
When using the Shopify API, we found that it is possible to retrieve the transaction fees, but only for some gateways (e.g. PayPal, Shopify Payments, etc...). I'm not sure if Afterpay's fees are available...