I suspect it's to do with branching. I've never encountered it as far as I know on R4 DVDs, but I think it's more prevalent on R1. When Alien3 got recut, I think R2 and R4 got a seamless cut, but R1 got a branched cut, where the film would cut to added scenes elsewhere on the disk. This lead to Murphy in the vent calling for Spike in the assembly even though he wasn't in the film for R1. In R2 and R4 that line is deleted.
This would allow for deleted scenes to be accessed separately.
Ah, I see. Thanks for humouring me and clearing that up.
On Anthology only the deleted scenes for Alien were viewable seperately (and perhaps some Aliens stuff via the LD archive).
I've not been through all of that stuff yet, but the Alien
LD archive does indeed include the deleted scenes. As an added bonus, the versions in there are the original takes, whereas the versions available for separate viewing on the film disc (in the Blu-ray set, although I'd imagine the R1 Quad is the same, based on what you've said) are the edited versions that were actually reinstated in the Director's Cut. Stuff like the transmission being
different and the cocoon scene being edited down.
As far as I know they're all available separately on the blu-rays.
The Blu-rays definitely have the scenes available separately; I checked during the process of trying to figure out what was going on.
That would also explain why Murphy calls for Spike in the Blu-ray version of the Alien 3
Special Edition when he didn't in my old DVD version.