Create Order in a custom app for store owner by Sachin

I am helping a store owner with 3 different shopify websites based on the physical stores. He would like us to create one custom mobile app which makes eCommerce possible across these three different stores. I was going through the api's and seems like it would be possible to highlight inventory/product details across these stores etc. However, when I checked the order api (http://docs.shopify.com/api/order), I see this: "The only way to create an order and accept payments via Shopify is by entering the storefront, adding items to cart, and completing checkout."

Does this mean that I won't be able to provide the consumers using the app to create an order for one of these stores in the mobile app?

Thanks!