A2X has been built from the ground up with one basic premise - to correctly reconcile all transactions back to the money in your bank account - as this is one data point that you can have confidence in.
We have found that, when doing Amazon accounting based on order data, it is extremely hard to ever correctly reconcile to the payments in your bank account. All of the fees, adjustments, reimbursements mean that the order data seldom relates directly to the net payment Amazon pays you.
In addition to the goal of reconciling the payments from Amazon to sales and fees, there are two other reasons we are not importing individual invoices:
1) QuickBooks recommends against having too many transactions in your accounting system - QuickBooks Online is designed for financial reporting, not for operational functions.
2) We have experienced that, as your Amazon business grows, it becomes increasingly difficult to manage the large number of invoices, as well as it becomes less useful for management reporting.
For example, if you have 100's of orders per day, you likely do not want to review each one of them within your accounting system, however, you do need to have a complete confidence that Amazon paid you the correct amount, and that this payment reconciles correctly to your sales and fees.