@Bealdwine You should try asking in the Wrye Bash thread. I'm sure someone there would know. I would like to know the answer to that too.
Edit: Refer to the post above. Frihyland posted it the same time I posted this... weird.
About tricking Wrye to install in main skyrim game directory, will it work if you added /Data/Root to actually point into the main Skyrim game directory (as suggested by MontyMM), put a folder named 'Root' in a BAIN arhcive, put files that need installing in the main skyrim directory like RCRN inside it, tick has extra directories, then install?