Thank you for responding, Lawrence.
I switched to Premiere during the FCPX update fiasco, so I’ve let Compressor go too by now. Any experience doing this in Media Encoder or Premiere?
Honestly, it’s also hard for me to believe that FCP can do something like this and Adobe can’t these days. Just to clarify, you can add chapter markers in FCP, then export an mp4 with H.264 codec, open that file in Quicktime and use the chapters?
Also, how have you used Handbrake to do this? Do you transcode a QT file to mp4 and it retains the chapter markers?