Re: A beast of many things...
a freaking filesystem, because that's really what PDF is
When you want to flatten complex documents into a single file, you're probably going to end up with a compound file format of some sort. Open Document Format is a compound file format - it's just a zip archive, in fact. OOXML and XPS are compound file formats. EPUB is a compound file format.
The alternative is a single non-compound format that encompasses all the types of data you might want. That's worse: it's more cumbersome to define, document, implement, etc. With a compound file format, it's trivial to build toolchains that operate on only some parts of the entire document - the explode / filter / implode pattern.
HTML and its siblings can get away with not being compound because they present a de facto remote filesystem to the user agent. They don't try to flatten everything into a single byte-stream blob.