Well, it seems like you may have had the same idea as I did a while ago - I thought about layering the theatrical BD over the Extended one for the Theatrical scenes and then setting the blending mode of the theatrical BD video to color but I did some tests and it wasn't quite so easy, because the cropping is very different, where the OT BD is more cropped on the right and less on the left than the EE BD (or the other way round, I don't temeber exactly), so you have to crop the EE footage quite a bit for this approach to work, plus the cropping difference isn't consistent troughout, so you'd have to readjust the overlay shot by shot and even the warping is slightly different, so this approach is problematic at best.