Zombie, I'm not sure if it's been brought up here at the boards yet, but there's an interview up at thedigitalbits with the answer to your question about the Apocalypse Now BD.

http://thedigitalbits.com/articles/apocalypse/interview01.html

Basically they scanned the 2001 IP (The Redux IP), restored and color-corrected it and, for the '79 version, simply conformed it to that edit. Since it's a relatively simple difference in edits, both versions are seamlessly branched onto a single disc. I expect that BD-50 to be packed to the brim!