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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.




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