We're on the same boat here.  We're heavily using Commerce for inventory management on Shopify and Ebay as well as purchase order, wholesales invoicing for our customers.  QB should at least provide detail instruction on the migration steps for those who are on Commerce and moving 'some' functionalities to QBO with E-commerce accounting.  QB provided the instruction to backup and what do you expect us to do with that.  I don't imagine to be able to import these data into QBO seamlessly.  

I have asked supports multiple times and didn't receive a direct answer on what to do with our Commerce data and functions to handle our ecommerce business moving forward with QBO.  I haven't tried the Inventory tracking within QBO yet but sensed that this function is very limited and not even close to commerce inventory control.  That probably the main reason QB is dodging to give us a straight answer.