The naming convention cannot be changed for built-in colors since these variables are tied to multiple elements throughout the templates. It is also important to keep them generic and not tied to specific names (i.e. blue, green, etc).
You can add additional color variables, but the majority of elements are still mapped to the base set defined in the Style Guide. To do this we would add additional color variables to the custom template and reuse those variables as needed.
Typically, three colors are usually plenty, and keep in mind you can modify base colors as well. For instance, if your brand-primary color is blue and you wanted a section in the site to use a shade of that blue, there would be no need to introduce a new color to the palette for that shade. We would simply adjust the brand-primary using LESS.