UPDATE: The new Alpha pre 2 version works flawlessly with regard to getting textures from the MO virtual directory. You need run NifSkope from MO and then go to ...
Options > Settings > Resources > Paths
and let it autodetect your game directory (which will supply paths to all mod assets from the MO VD) and then let it autodetect your archives ...
Options > Settings > Resources > Archives
You will get all of your custom mod assets as well as any vanilla stuff that is not modded (I assume that resource prioritization adheres to game rules as managed by MO, and testing seems to indicate as much).
The interface is also much better in the Alpha version.
The devs have done an awesome job!