Hello,
Sadly we haven't found a way to implement this functionality yet. Due to how color palettes works in CKEditor 4, the underlying Rich Text functionality of the application, we can't have one color palette per theme. Nor simply have one working for both light and dark theme.
For your information we are working on another application, Notes, that would conveniently replace Code / Markdown and Markdown Slides, while also proposing some kind of light markup features like our current Rich Text application do.
