New Post: 2 Feature requests: Commercials as chapter markers and loading the .SRT into the MP4

Not sure if this helps or not,

But looks to be how they did it with handbrake, but it is Greek to me :)

http://sourceforge.net/projects/mpeg4ip/forums/forum/59136/topic/1837284 This link appears to be the code...
Changes between 0.8.0b1 and 0.8.5b1

    Core HandBrake Changes 
161         + Added: iTunes-style chapter markers. 

https://trac.handbrake.fr/changeset?new=1928&old=422

Hope that helps