Been reading all these for some bedtime stuff - keep 'em coming!
The gorge always struck me as something that was butchered in the final rush of development and never really appeared as I think the developers had envisioned in any version. Interestingly as you mentioned it does seem that the gorge texture itself follows along with where they intended to put bottlenecks for puzzles, which are present in the walkthrough but never implemented (although the pieces of them are there). Personally I feel that the early version dirt road (before it ended up as the B96 broken one that climbs the mountains) was meant to be there as such a thing would likely exist for the workers building the monorail, and to act as a guide for the player through the level. The broken-up roads in the final build seem to have been just thrown in without much thought on top of terrain that by this point was so jagged it all ended up looking extremely ugly. You can totally tell where the terrain was hastily raised late in development to close off the majority of JR.
I wonder, do those patchy B96 JR roads match up with any of the earlier terrains? That might give us a clue as to when the terrain was made the way it is in B96, as it's possible those roads were added before the terrain was made so rough.
Never really knew about the tar pits, thanks for posting that one - that was the kind of thing I was hoping to see more of.

They definitely look like tar pits to me, though it seems they were never actually implemented into the game anywhere. Funny that they did seem to make all those assets, though...I bet those tar pits exist on some dusty old hard drive somewhere. It seems to me like this scene uses assets that were possibly intended for the game but never made it in, or were replaced by improved versions (as with the skeleton). That "red machine" is an odd thing, for sure...perhaps some kind of early Geo Plant asset, as you suggested, along with the View Building. I find it odd that the developers made these assets but never implemented them, unless of course they're in like Build 005 or something.
I believe the patchy area at the end of PV is simply a byproduct of the developers hastily adding in the mountain to the north of the Geo Plant, as with a lot of the odd jagged terrain that occured by B96. It seems they noticed how poor it looked and tried to disguise it with some sand objects, unlike what JR ended up looking like.