I'm using MarkdownEditing v. 3.0.2 and Sublime Text 3 (build 4113) and MonokaiC color scheme is not applied. I guess it is due to the fact that it require Markdown GFM syntax being applied to Markdown files, however there are no Markdown GFM syntax anymore in new releases (only Markdown and MultiMarkdown).
However, the syntax highlighting is not working for me, I followed the readme file to use the theme and everything works fine except for the syntax highlighting.
I'm using sublimetext 3 on win 10 64 bit os, thanks!