Correct, CB uses its own language system at this time. We plan to move to Joomlas with CB 3.x after we've developed our new framework library to handle all the features we need and use since Joomlas language API is nowhere as powerful as CBs (we support one-to-many translations, string fallbacks, substitutions, and more).
This still shouldn't be an issue for you though. I'm not sure how you're handling multi-site, but if they're on the same server you should be able to use a symbolic link to link the folders.