AWS was built in the same datacenters by the same IT engineering team that provided core hardware and networking to the retail website. The top level software APIs were (obviously?) not created before the Amazon retail website.
Amazon IT and AWS invented a virtual machine infrastructure that Retail used as soon as it was available. AWS services were quickly adopted by many teams as well.
AWS has always beeywn the future of Amazon Datacenter IT. Retail is a huge legacy system, so of course Reddit could launch on AWS faster than Retail could fully migrate.
AWS is an externalization of core Amazon technology. Don't get hung up on the fact that Amazon runs on a babysat patched alpha version released before the 1.0-quality version went public. Retail needs some customizations hat your startup doesn't. Really.
This "skunkworks AWS" meme is a story about the business, not the technology.