Using MKVToolnix I would like to mux a commentary audio track along with a video track (which already includes it's original sound track) into one mkv container. However, the audio commentary track is about 10 seconds longer than the video track. Is this a problem? What would happen when the video is "over," would the 10 second remainder of the commentary track keep playing? Most importantly, this wouldn't affect the original audio track in any way, like making it go out of sync or something?
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No, yes and no. At least that's what happens when the audio stream is longer and I play it with MPC-HC.
Just remux the MKV with the additional audio. It won't change the original file so you've got nothing to lose. If you're not using a video player which lets you choose audio tracks in an MKV you can always replace the original audio with the commentary track, resave it as a new MKV and keep two copies of the video, each with a different audio stream.