Nick -
1) There are other companies doing this, but not on a large scale. It was part of the original business model for Method - we just haven't emphasized it.
2) Yes. When QB is closed you are inserting, updating and viewed cached data from QuickBooks. As soon as QB is open and connected to the sync engine, all changes get updated, bidirectionally.
3) Multiple files is not a problem. But the sync engine has to conform to QuickBooks rules. There's no way to read and write to a QuickBooks file unless QuickBooks is open. The Method Sync Engine uses the QuickBooks SDK - which means we interact with QuickBooks data via their interface, instead of their database directly. Even in "unattended mode" where QuickBooks appears closed, it is in fact open. Also, only one QuickBooks file can be opened at one time for QB SDK integration. So our hands are tied, as are any other developer's hands that wants to interact live with QB data.
Keep in mind you'll need one Method account per QuickBooks file, and you'll need at minimum Method CRM, $25/account/user/month. If you are talking about significant scale (>100 accounts), then there are certain scenarios where you can just use the sync engine, and not use the CRM interface, which is much a lower cost. You'll have to contact us over the phone to discuss this as an option if you want to go this way.
Paul