Wondering how other businesses  or those in charge of IT handle situations which I would assume are quite common:
(1) Company A has a brick and mortar location with an inventory management system, POS, and accounting functionality (let's call this internal software B)
(2) Company A wants to sell online and automate a lot of the purchase processes for their customers but is still limited by a lack of integration between internal software B and GrandNode for instance.  

We anticipate stock levels to be completely out of sync for the most part.  We may opt to not display stock prices if that is a possibility out of the box with GrandNode.  Additionally, when generating invoices, packing slips, and shipping with an online store - almost always we anticipate the manual entry of this order to occur in the internal software B first.  However, does this put automation at risk?  Is a customer alarmed when their invoice isn't emailed to them directly after payment?  What about backorders?  Typically when orders are received we do not obviously charge for back ordered items until they are shipped.  

How do other folks handle a lot of these situations?  I am hoping we are not entirely unique in this instance.

All kinds of synchronizations and integrations can be done using the Web API, which is available on the marketplace. It's probably the most efficient and easiest way to synchronize and integrate 3rd party softwares with GrandNode.