MC
does already support MP4s and MKVs with chapters, like it does with DVDs and whatnot. But those chapters have to be added to the media file itself as a track when it is created. So, it seems like you mean that you want MC to allow you to create chapters in files that don't otherwise have them embedded. Right?
Well... You can do that too! Sort-of. Disclaimer: I haven't played with this much at all yet, personally, but I have read lots of the threads and followed along. I think using it is still a little clunky, but... MC 17 has a new feature called
Particles which can be used for things much like this. Particles are like "virtual copies" of a particular file, which can each have their own playback range and other characteristics. It is a new feature, and (like I said) I'm no expert, but others could comment.
Try searching Interact for "particles". Here is the wiki page:
http://wiki.jriver.com/index.php/ParticlesOne thing to note: It isn't quite chapter support. For example, because you'd then be playing a "playlist" of separate "files" in MC to play through the whole thing, I'm not sure how seamless playback switching from one "chapter" to the next will be. My guess is that it would be something like switching from video to video in MC now. Very quick (if your disk is fast and not sleeping), but still there is a slight blip as it switches. But, maybe not... Someone who has used them would have to chime in. If so, then this system really might just be better suited to things like are described on the wiki page: Chopping up episodes on a TV Show DVD, or separate songs/movements in a live recording.
For things that are actually like chapter support, MC does also support sidecar EDL files (used for commercial skipping and generated by something like comskip). With this I really haven't played with it at all (I really need to get around to that one of these days), but
here's the thread where Matt introduced the feature. Search for more info. An EDL file could contain chapter regions, in theory, just as easily as they could contain commercials. And many video editors can output EDL lists from manually defined marks, so that would maybe be another way to do it. I don't know how well MC's commercial-skipping-focused EDL support would handle this, but it might be worth looking into as well.