MKV2VOB works well if you have parallels or VMware. If not MP4Box works (but only 2 challen audio).
See my earlier post for more info.
Mike
MP4Box works great with TV Shows, with are usually around 1 Gb, but don't work with movies, that are at least 4Gb. You have to split the original mkv file to process it with MP4Box, and after you can cat the files togheter still using MP4Box, unfortunately the resulting file plays well in quicktime but not on the PS3, and I still don't understand why.
Anyway, you can have the multichannel audio using this method, basically you process the video as you described in your tutorial, for the audio part you open the mkv in quicktime (with perian installed), extract the Sound to Aiff, this will maintain the AC3 soundtrack, then open the Aiff in quicktime, export to Mov container, in this process quicktime will convert the ac3 stream to multichannel aac (6 channels), then you open the mov in quicktime, export to mp4 with passthrough.
Now you have an mp4 audio file with 6 channels, with the correct channels mapping, and you can mux it with the video using MP4Box.
I've done all my Lost and Heroes HD TV shows with this technique and they works great on the PS3. I'll try to tag one to see it the tagging works and I'll let you know.
Edited: Ok, I've tried to tag the Lost Season 4 Episode 1 I've made with MP4Box and Quicktime audio conversion and worked great. All the tags appear in quicktime, even the movie poster.