Quick question from a noob - how repackage back to MKV

Really cool work work on this, but I have no interest in repacking my final media files as MP4, and it seems pretty inefficient to run this flow then remux the MP4 back to MKV. I would really prefer to just keep everything MKV. How would I go about replacing the MP4Box step with mkv equivalent? BTW, I absolutely want to keep my TrueHD audio streams as well.

TIA!