Doesn't matter.
Adobe InDesign CS5.5 exports ePubs as a bunch of HTML files (don't know about 6.0 yet), while new projects in Sigil will be as XHTML, and FineReader 11 will also export ePubs that contain XHTML files.
ePubs can also be in XML format. See the screenshots from:
http://code.google.com/p/sigil/