Your understanding of .mkv is not wrong, and it is indeed possible to extract the video and pack it into an mp4 container instead, and for most releases, that would achieve that result.
For our release, it doesn't, because the video and audio files contained in the mkv contain two instances of some scenes, and the chapter file which is also contained in the mkv instructs your media player to skip over the version that you're not watching. And so if you just extract the video and audio and put them into an .mp4, you'll still get two instances of those scenes, but your media player plays both of them too so that's not what you want. In order to get an .mp4 which works the way it's supposed to work, you need to re-encode the video using something that can read the mkv chapter files and skip over the wrong version while encoding, which is possible but I don't know how, other than this method >>14290
which is inconvenient and takes a lot of work.