If you update index.html and style.css, GitHub pages will apparently publish them simultaneously (atomically), but with S3 you upload index.html, then style.css

If you update index.html and style.css, GitHub pages will apparently publish them simultaneously (atomically), but with S3 you upload index.html, then style.css — one of them will be "published" later than the other. (Analogy: GitHub pages is like creating a new directory, putting files there, then renaming the directory to the old name; S3 — putting files into the old directory.)