Should user settings take precedence over custom themes?

I am building a desktop application that uses HTML, CSS and javascript, using the Electron framework. My application has the ability to let the user add a CSS file to style the application, the way they want it.

I also provide a separate window for letting the users change more aspects of the application(without the need of writing CSS).

They can change the following things:

  • Background color
  • Text color
  • Font size
  • Backgound image

Now my question is, what should take precedence over the other? Should I let the user settings be overridden by the applied CSS file or should the CSS file be overridden by the user settings?