Currently AWS S3 deployment of Guise sites supports collection content in the traditional way by deploying e.g. foo/bar/index.html for content and not deploying anything at foo/bar/ (i.e. skipping collection deployment for S3). The S3 bucket server will transparently serve index.html content for the collection.
But in S3 resource paths are arbitrary object keys, so there shouldn't be any problem actually deploying content to foo/bar/ and not deploying a foo/bar/index.html resource at all. This would better reflect the semantics of the site. It is unclear if pragmatically this would bring any benefits, but it's something to explore.