WP-Skeleton/Bedrock support in EAP

I primarily use Bedrock https://github.com/roots/bedrock as a base for my Wordpress development, which is similar to Jaquith's WordPress-Skeleton: https://github.com/markjaquith/WordPress-Skeleton

A look at the folder structure can be found here:
https://github.com/roots/bedrock#folder-structure

Has anyone managed to get the WordPress support working with an unorthodox file structure?