Wouldn't it make more sense
to simply record the two images as two image streams? They're definately not pressed for storage space and it would mean that the consumer could use their preferred medium. So you could use Anaglyph, I could use my HMD, Tim in Accounting could use shutter glasses and Joe Bloggs over there could use his £KLots autostereoscopic display. Given the two video feeds it would be really easy (hence cheap) for the Player to have a lot of built-in playback options.
Plus it'd ensure that the disc was entirely compatible with the older 2D Blu-Ray players- it'd just be two blu-ray movies on the one disc.