With current Custom styling implementation, customers has to make following two custom changes in their App after importing the theme module:
Refer following documentation https://docs.mendix.com/howto/front-end/customize-styling-new/
Current implementation adds some manual work to customers and this can be reduced/automated by changing the framework implementation to automatically take variables defined in themesource/mytheme/web/custom-variables.scss as high priority and the App styling should be based on these variables. If no value defined in themesource/mytheme/web/custom-variables.scss then only it should look for variable value in theme/web/custom-variables.scss and also remove the import of custom-variables.scss from themesource folder into custom-variables.scss of theme folder
In summary, customers should just import the theme module and set its order in App settings and should not make any code changes as mentioned above to theme module in their App.