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.
It’s not CentOS 3, it’s CentOS with Linux kernel 3.10 (a 2014 kernel). This was supported in RHEL/CentOS through 2017.
Still very dated and a bad idea, of course. And even weirder that it’s on a new machine. I’ve seen tons of stores using Win7 past it’s EOL, but on older hardware.