Earlier quoted context omitted.
We do the reconciliation—and you're exactly right that QBO doesn't have a reconciliation API, so we have to do it outside of QuickBooks in our own system. (But yes, we've found that if you don't do this reconciliation, the bank feed will just silently drop transactions, etc.)
Can you clarify a bit more when you say you reconcile "outside of QBO"? Does this mean you're keeping track of reconciled items in a separate system and not in QBO? In QBO if an invoice payment is reconciled I can see which bank transaction it has been associated with; will this be the case with Pilot?
Can I encourage you to drop me a note at waseem@pilot.com or we can schedule some time together here?: https://calendly.com/pilot-waseem/overview