You have it backwards. AWS didn't solve anything for Amazon internally (it's actually kinda funny how tricky moving internal systems onto AWS is). FBA and AWS are Amazon taking systems that they already had to build for its own use and selling them as a product/service to external companies. FBA is just a way to use a portion of Amazon's existing distribution system. AWS is a way to use Amazon's existing tech platform(s).

Fulfillment solves warehousing, inventory, and delivery of Amazon packages. Amazon built out their own network. FBA is Amazon renting out that network to third parties - whether they sell on Amazon or on their own ecommerce site.

One possibility related to commingled SKUs would be that they can control coverage of items in warehouses by controlling which warehouse(s) sellers and their product to.