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You can just use MKVToolNix to add the second track to the MKV file after rendering, it’s still another step but doesn’t require re-encoding.
If you’re just trying to multiplex tracks and not actually edit the video, I’d recommend doing it entirely with MKVToolNix and skipping Kdenlive for this use. I’ve done this previously to combine a subbed video and a dubbed one into one file, you can offset or stretch the audio if needed as well.
Not rendering. Muxing, which is short for multiplexing. Lots of software can do this, including MKVToolNix, ffmpeg, and GPAC/MP4Box. If you’re also encoding the video, Handbrake could do the job.