Encoding/Compressing Recordings with Chapter Removal

Has anyone found an app (Handbrake, for example) that can work with the way commercials are marked and encode/compress the video without having to manually go through and mark off the commercials?

See this thread View Tivo Recordings

The ffmeta and ffsplit files are in the Logs/comskip/xxx directory next to your TV and Movies folders

I just use MceBuddy.