I just recently created an experimental epub from the sphinx documentation.
in a simple theme. I did not have to edit the created HTML files.
The tedious part was creating the meta infomation contained in the files
content.opf and toc.ncx. I actually edited the files by hand, although
in principle sphinx could create the files.
I attach a diff that contains the local theme and the tar containing the
meta information needed for the epub. Extract the archive in _build/html
and run build.sh to recreate the epub.