This article should be reworded slightly. The point it was trying to make is if you want to use these plethora of payware video editing software packages that has limited support for MKV, then install CCCP and viola they work.
However, what people should be doing is, extracting the contents of the MKV container, and using all those tried and true tested editors that everyone already knows how to use, do the edits, then create a new MKV.
Here is a better list of tools
1. mkvextractgui-2 (extract those video clips to .h264 .mpg .avi, audio to .aac, .mp3 .ac3)
2. FFMSIndex, DGIndex, DGAVCIndex (Frame Accurate decoders for avisynth)
3. avisynth (frame serve those video clips, crop, resize, cut, splice, filter, countless plugins)
4. Lagarith codec (lossless video compression for working files)
5. Virtualdub (Create working files for Editors, or use it to do all your edits not done in avisynth)
6. AviDemux (like Virtualdub, with perty buttons, Comes with extra tools non video related)
7. Adobe Premiere,Sony Vagas,Pinnacle Studio,Lightworks,VideoLAN Movie Creator (Editors)
8. Subtitle Editor, Aegisub, BDSup2Sub (Subtitles)
9. Handbreak, MeGUI, AVStoDVD (use Editors videos, creates your MKV, MP4, DVD, BD)
Handbreak, MeGUI can do some basic edits, like combine, cuts, and the sort, but this article was trying to talk about tools to do effects, transitions, annotations that Editors will do. If you need basic stuff, then there are plenty of FREE tools that will get the job done that I might not have listed
MKV vs MP4, MP4 supports 1 video, many audio, text based subtitles, simple chapters, MKV supports many video, many audio, fancy and text based subs, fonts for those fancy subs, warp point chapters(load external file play it, then continue playing current clip, useful for episodic shows with same opening sequence) and anything else you can throw at it.
~Majorlag