I've a multistore setup which is using a custom base theme for the structure but the colour scheme is to change per store. Is it possible to fall back to the base theme but only modify _var.scss per store?
You can use RWD as your parent and base your multi store themes off of this using Magentos theme fallback
This is a really useful step by step guide on how you can achieve this
Yes this is possible using Magento it's fallback system. In your new theme with the seperate color schemes you can define a fallback in a theme.xml.
There might be more useful options out there but this is the only obvious way I know.
For more information on theme fallback please refer to http://alanstorm.com/magento_infinite_fallback_theme_xml