Subversion(SVN) tracks changes at file level and as long as what you're keeping in the repository is the EPUB file, it will only track that file(as binary). It's true that the EPUB file is a container(with files) but SVN does not handle this aspect.
If the files contain work in progress I'd recommend keeping them outside of the EPUB on the SVN repository. Besides, with a simple script an EPUB can be constructed at any time from these files.
We frequently encounter people keeping their work in progress in EPUB files. Don't get me wrong this is quite possible and even preferred if you only need your work in one format(EPUB/XHTML).
However, it is generally good practice to keep your content in a more flexible XML document format(e.g. DocBook, DITA) then process that content into published formats(PDF, EPUB). This allows a lot of flexibility when a new published format appears or when you need to republish your content with a new formatting or layout(different headers/footers, decorations, etc).