Firstly, thanks a lot for creating this plugin it makes it so much easier for getting a cleaner output.
I'm having a few issues with the alienship theme and the roots plug. It is somehow breaking the theme and creates a few anomalies.
This is the default theme without activating the plugin
When I activate the plugin, the following issues are observed
For the footer, when I resize the window after adding a background colour in the Chrome Inspector, the background snaps with some margin space
I initially checked with the alienship author, and he suggested to check with the roots plugin author and if an extra fix can be done with the plugin to properly rewrite the URI for the standard WordPress style.css
I have prepared a test wordpress server if you need to access. It could be easier that you see the demo and have a look!