Bumping this thread (I know there are many other like it based on a search).
As of version 15 of XBMC/Kodi (Isengard alpha 2), Video chapters are supported:
http://kodi.tv/kodi-15-0-isengard-alpha-2/
It would be great if the issue described in this thread and others (such as /t/14808/1 ) around mp4 chapters resulting in mp3tag not being able to tag gets resolved.
Thanks,