The guy who made MultiAVCHD wrote up this tutorial on creating branched BD playlists:
http://forum.doom9.org/showthread.php?t=154815
Basically you create each 'chunk' as a separate BD folder, then use MultiAVCHD to link them into alternative playlists (then use BDedit to remove redundant elements).
I've used this technique to link separate elements on a multi-part Blu-ray (e.g. a new logo before the main feature) - it's the best way I've found to create such compilations without actually editing them together (and thus reencoding). Might be worth a try, but results do vary from one BD player to another.