Thanks for the tip on the "river past vid cleaner" tool, I'll have to look that up - I have been using DVRMSTools to strip commercials and convert from DVR-MS to MPG, then Handbrake to convert from MPG to MKV/x264, but handbrake is a pretty manual solution, will have to check out river past.
I *think* DVRMS can be configured to convert from DVR-MS to MKV/x264 (using ffmpeg or x264?), so that the commercial stripping and transcoding can be done in one step (and automated, to boot!) but haven't been able to figure out the profiling necessary to do so.
re: control of the playing back MKV - I, too, miss the REW/FWD options with non-DVRMS formats ... MCE doesn't support MKV anywhere near as well as DVRMS. But I don't think you can have it both ways .... DVRMS and MKV are "container" formats - each container uses a different codec to encode the video, DVRMS uses only MPEG, while MKV supports multiple codecs (typically AVC/h264, divx, xvid). These latter three codecs are much more efficient at compresing files than MPEG, which is why you get a much smaller file. But if you converted your MKV back to DVRMS, it would require transcoding back to MPEG, which would get you back to the near-original large file, you'd be back to where you started, with slightly less fidelity becuase of the two transcode steps (MPEG to h264 to MPEG).
re: metadata - I believe one can embed metadata into the MKV container, but again MCE will not render the info. I make up for the loss of the metadata embedded in the DVRMS file by using media browser (launched from within MCE, and fully controllable with remote cotnrol), which uses its own mechanism to pull down metadata from thetvdb.com