A and B are YCM duplicates on Estar base for maximum alignment. In short, 3-strip positives are what goes into the optical printer.

White parts of C and D are effectively transparent, but of course the black parts aren’t perfectly opaque (or we wouldn’t be seeing garbage matte artifacts all over the OT, now would we?).

Ordering the elements is carefully planned as the optical work-- essentially a very fancy double-exposure process-- can take up to 10 hours (maybe longer) depending on the complexity of the shot. Using just one background plate and foreground element, it might go like this:

The B&W matte and inverse matte (just calling it that for the purposes of this post) are put into the printer to calibrate alignment.
The YCM background element plus inverse matte (where the foreground object is black) is photographed in the printer.
Film is rewound. The YCM foreground object plus matte (where everything around it is black) fills in the blank, unexposed part of Step 2.

For the OT, plates were filmed in 8-perf 35mm (VistaVision) and the final composite would be directly photographed onto 4-perf anamorphic 35mm in the optical printer. This is considered one dupe generation with the only steps being Negative(plate)-YCM-OCN(composite).