"All the bonus feature" often involves doing a "Backup" rather than ripping to MKV. MKV files do not include things like picture-in-picture and similar that some BDs take advantage of.
If you're interested in the commentary audio, make sure that all audio tracks for your language are selected when converting to MKV, and you will be able to switch to those audio tracks in your playback software. See this topic on how to select the various audio/subtitle tracks:
http://makemkv.com/forum2/viewtopic.php?f=1&t=16405