This issue was marked "solved" in another thread. That was a lie, because it was not solved to anybody's satisfaction.
It's critical that you actually allow payments to be made that aren't just the amount for the invoice on manual or draft orders. For example:
1. Taking a deposit on an invoice and marking it partially paid2. To account for external payment mechanisms and the variability of exchange rates (or just user errors)
"Capture order payment" is totally insufficient. There are times where the amount paid is greater than or less than the exact invoice amount. Like, I've come across it four times TODAY.
Otherwise, Shopify's listed transactions just do not reconcile with the bank account and there's no way to fix it. No, "buy another subscription app" is not an acceptable response. This is a fundamental feature necessary to keep book keeping correct, not a "nice to have" option.