My 2 Cents
Calibre all the way. Edit your TOC in Sigil, let Calibre do the rest. If your "producing" a novel for Kindle you will need to do a little code scrubbing though, Calibre is intended as a library. It just gets you very close to what you need. All hail Kovid.
Kindlegen



is truely awful in to many ways to mention. It's sole purpose, I beleive, is to force inexperienced (no disrespect intended) self-publishing writers to produce bland featureless text only books with no professional looking formatting. After all, if we could all produce content to the same market standard why would we need publishers and publishing services.
Sorry, my cynical gene kicked in there.