Have you tried using the “product shipping required” field to check for fulfillment?
That’s the main way people fulfill digital products with Order Automator. I would expect you can access that field in Flow as well, try using that.
The product shipping required field is in the Product admin page, that’s what makes it a digital product. I would think Flow would have that option.
Then just make sure the location you select to fulfill from is assigned to that product. Check the Inventory section when on the product (or variant) page in the Shopify admin.
If you’re not using product shipping not required for some reason, then just match up the SKU, and fulfill from the location the product is assigned inventory.