I saw a very similar post from 2013 but no concrete answers were given, so I hope at this moment, there must be some solution. There was a suggestion for an app, but the link doesn't work anymore.
Basically, I need some sort of accounting software that will integrate my company selling online, offline and retail. So if I sell an item online, it will deduct from the inventory. If I sell the item offline, it will deduct it from the inventory, if I sell 20 items wholesale, it deducts them from the inventory. I also need to be able to have different prices (online, retail, wholesale).
I also need to create invoices if I sell it offline. And if I purchase a batch of products, I need it to add to my inventory.
I am not sure if this actually answers your question, but it seems like a relevant feature of Shopify that may help solve at least some of your needs. Admittedly, this is more about inventory than accounting, but you should probably check it out: