Not exactly. The way I see it we’ll ship the app with an actual SCSS file and it will be compiled to CSS at run time (and cached to disk). Compiling at runtime means the generated CSS is dynamic, based on the current theme.
So in the repo there will be one master SCSS file that can easily be tweaked, and theme.js will contain the variables that change from one theme to the other. Custom CSS will still work the same - it will just be applied like now, after the SCSS and theme has been applied.