In the manual Website Theme, it is suggested to change the website theme by modifying scss files.
If you take a look at the default theme generated by the configure dialog, it imports
erpnext/public/scss/website. These are the default theme files for
erpnextapp. You can remove them if you want to write all of the CSS by yourself.
However if we do it, then during next update it conflicts with the repository code. Ability to change the look and feel is important for websites and so are updates. I believe that erpnext should refer to scss files through links. If one needs to change the theme, then they only need to change the reference to the link. This way both website theme can be changed and there will be no conflict during update.