I think it could be done even with free software - MultiAVCHD; here you are a guide to make a BD with two different endings:
http://forum.doom9.org/showthread.php?t=154815
Probably this guide is useful to make alternate crawls instead endings, but you need a lot of patience, and a good skill.
I strongly wish you could achieve your goal; if you will find out how to make a working seamless branching BD, PM me as I could provide VHS Hi-Fi italian tracks for all the three movies, OT and SE.