If you want to consider that single or multiple files ... quickly veers into semantics.
I'd argue that that's not meaningfully different to OP's suggestion of a HTML file with all the content inlined, though. It's still a single file grouping everything required together and can be easily edited and read practically anywhere. It has a few advantages over the inlined-content HTML file, too:
- You can read the compressed file directly, an epub being typically half the size of the uncompressed files (going by a quick test of 30 randomly-selected files I had on hand).
- Storing the actual JPEG, PNG, OTF, etc files inside the zip is more efficient than inlining them as base64 and then making the browser decode them, in terms of both speed and filesize.
- While reading an epub, different sections can be a different HTML files, and only one needs to be loaded into memory at a time. This can be irrelevant for smaller things but it can make a big difference sometimes--with pages that include many charts and tables, documentation for graphics libraries that include images and animations for each documented function, etc.
- Epub files have native support for highlighting and bookmarking, to keep your place in long documents and share the file with your highlights attached.