Documentation rendered HTML reads the global style from scdoc.css, but also reads frontend.css and custom.css (in that order) if available. This is to enable specific frontends and allow users to override the CSS.
So to customise the CSS, the user can create a custom.css in their SCDoc: *helpTargetDir or at the root of any HelpSource directory (for example in YourExtension/HelpSource/custom.css).
Colors are defined as CSS variables, so that to change any color, it's sufficient for a user to override the relevant variable in their custom.css. These variables are then used to set any color in all other css files of the documentation.
Specific variables are not reported here, please refer to the default CSS theme for all their names and default values.
The themes directory also contains a README.md which goes more into detail about how a theme gets applied and stored for a client and how a theme can be developed.
CSS themes distributed in HelpTargetDir/themes are provided only to match ScIDE's UI themes. There is currently no implementation for modifying CSS themes dynamically or to add custom ones, so for any customization it's recommended to write a custom.css file as explained above