Cloudfront/s3 options, do I need them?

My site already integrates Cloudfront and s3 for speed. I have a subdomain with cname redirect to my cloudfront/s3. My s3 bucket contains portions of wp-content and wp-includes. This is setup for performance improvements on my site. I plan to block portions of some posts, and some posts/pages and comments on my site.

Is there any reason for me to use the auto-create/integration in s2member “download options” or is that only used if I actually plan to have ebooks or other downloads for offer to users that I want to restrict?

Right, you only need to integrate s2Member with S3 to protect the downloads from there. If your files are public, you can use S3 normally, without integrating to s2Member.