I'm hoping that someone may have encountered this before and has a clever workaround (or better yet, knows of a way to actually fix it instead of working around it).

We have two websites run under a single company. We have been able to set the "from" email address for most of our transaction emails on a per-site basis under Setup -> Website -> Set Up Website -> (domain) -> Email tab, but the final billing confirmation that is sent after the order fulfillment message seems to be controlled by the settings for our single company.  To clarify, all of the emails except for the final billing confirmation seem to be able to be set on a per-site basis - is there a way to make that last message come