Yes, custom styling should still be added to the custom folder. But instead of going through all the empty selectors in the files, we think it is cleaner and more clear if you add .scss files with your custom styling. This way you can easily see the styles that have been overwritten or added.
Our ideal workflow: You add a .scss file of what you want to change (example: buttons). And then copy/paste the selectors you need of what you want to overwrite
The new Atlas UI theme has only the custom.scss and _custom-variables.scss. The custom folders you're refering to are from the old Mendix UI Framework.
Custom SASS should be added to the Custom folder and included in the custom.scss file.