So What’s Wrong with the Graphics Pipeline?
Well, it’s a pipeline. You can’t send something back for a change if a later stage reveals the need to. A good example of this is how games through the ‘90s had a lot of trouble representing transparency. Things you were supposed to be able to see through, like shallow water or smoke, tended to look solid, or flicker in and out.
Once raterization decides something is behind something else, the thing in back is pretty much gone. You can’t get to the texturing part and say “Hold on, this thing is smoke, you should be able to see stuff through it."
So a person standing in shallow water would have their legs ‘behind’ the water, and you wouldn’t see them at all. A plane flying though a cloud would look like the cloud had a hard edge and the plane was coming out of a cloud-shaped gate from another dimension.
The trick used was to animate in the opaque surface, using some frames the opaque water or smoke, and some with what should be seen through it. If it didn’t come off just right, it would create a flickering effect. A more sophisticated trick was to make smoke a bunch of dots, and you could still see the background depending on how dense the dots were.