I'm finding this discussion interesting since a client of mine that was thinking of integrating its QuickBooks accounting system into Drupal Ubercart (QuickBooks is one of the most common North American accounting packages for small organizations, both for profit and non-profit.) The initial spec was to continue with the accounting package being the system of record for the client and invoice list. But they've asked for another look at this, and are considering moving all of the details about clients and invoices out of their accounting system and into a billing system, whether CiviCRM, Ubercart, or a more specialized system like Freshbooks is still to be determined. On this approach, the accounting system does not track clients and invoices. Instead, it would just get batch totals with the aggregates for each income line - events, grants, rent, etc. - and wouldn't be responsible for the fine details of Accounts Receivables.