There are actually additional sourceSets that are available. You can do this:
src
|__ main
|__ flavor1
|__ flavor1Debug
|__ flavor1Release
|__ flavor2
|__ flavor2Debug
|__ flavor2Release
|__ debug
|__ release
which I think will give you what you want -- inside one of the flavor + build type folders, you can have your variant-specific resource in the appropriate resource subdirectory.
See the docs at http://tools.android.com/tech-docs/new-build-system/user-guide#TOC-Sourcesets-and-Dependencies for more information.