Chapters are just an attribute, like all other attributes. Looking at the database, the name of the attribute should be something like:
To try it, go to MediaFilesSync in the web admin, and browse to the media file. Then either edit the attributes that are already there, or add new chapter attributes and fill them in.
This is just going off of what I see in the database though, so I don't know if the timecode is truely parsed or not. I've never tried this, but its wirth giving it a try!