Why ZIP versus something like TAR?
TAR is a 'Tape Archive'... the metadata for each file is adjacent to the file contents itself. (Which is what you'd expect for a format designed for a linear access media like tape.)
For ZIP, there's a single unified directory structure that can be used as an index into the file.
> A single unified directory structure does seem like a desirable feature,
It can make it more difficult to incrementally stream out an archive, so it's not a complete win.