Comment by thomastjeffery
9 years ago
MKV has more features than MP4.
Whenever I remux MKV->MP4, I lose chapters.
Technical superiority is more important than compatibility, especially when you have MPC-HC and VLC that are happy to play practically any format ever.
MP4 also supports chapters; it's probably the muxer you're using that does not implement the feature.
But yes, MKV supports virtually any codec, so that is a big plus. It comes at the expense of support on different platforms.