I'll also note, part of why I think we're confused is that you haven't been very clear. For example, I'm not sure if you just made a typo here, but this sentence makes no sense:
2. I have an .mkv file ripped from a music concert DVD and it has a DD 5.1 soundtrack, so presumaly that's 2 channels.
You have a file ripped from a DD 5.1 DVD and it presumably has
two channels? Huh?
So... Assuming my guess of the re-encoding in MC's DSP isn't correct, then please just figure out what is actually inside the files you're using. FWIW, RipBot doesn't allow AC3 in MP4 because, while it is (now, not originally) officially supported in the MP4 spec, many popular players don't. Most notably, iDevices won't play AC3 tracks when using the built-in video players, and iTunes only supports AC3 passthrough (bitstreaming) and can't actually decode AC3. That's pretty common among the rippers out there. If they allow AC3 to be passed through to MP4, it is usually not one of the "default profiles" and you have to enable it manually.
Therefore, it is probably assumed if you're ripping to MP4 that you can't play back an AC3 track at all. If you ripped that disc, and it converted it to AAC, it
probably converted it to stereo. But MediaInfo will tell you what is inside it, so just look.
MP4 does "officially" support AC3, but many of the most popular players do not. I also believe (though it is hard to find good references now) that