EBM and Prophet's maps diverged a lot from my (very sketchy) brief. They were meant to be part of the same location, an outdoor map with ruins leading to a more intact temple that had been converted into a Skaarj base. The small area of ruins close to the beginning of EBM's map is the only real clue to this intended continuity. And, of course, the maps were most certainly not meant to be connected by a teleporter - a mechanism I'm often not keen on and didn't like in RtNP, as it feels like it invalidates much of the player's journey (I make an exception for the teleporter that links Outpost 3J to Velora Pass, as the Sunspire is clearly visible from the landing pad so you're still in the same general area as you were before).
Just wanted to expand on this. It's been years, mind you. Pretty sure the teleporter segway came about because I couldn't make heads or tails out of how to connect our levels. EBM's maps didn't have ruins. It had bricks and pieces of stone on the floor level of huge canyon walls. I liked his level, but the teleporter made it easier for me. I think I worked it into the concept too, with Location Z-14 being a sort of "teleportation junction" between Skaarj places of interest.
I used a different skybox because I was playing UT with certain renderer settings at the time and I hated the skybox in the other levels. Some of the maps used the alternate skybox mountains with the horrid black borders. I was also sick of seeing the same generic Na Pali skybox. But then again I didn't set the textures right in my own skybox so they have seams. Guess that missed fixing when the second version was made.
I remember Willis's map because I tested it with him, though I don't remember if many of my suggestions or edits made it into the final version. I don't think they did. Though I do seem to remember a dumb debug merc I edited for testing was actually used, which was not intentional and I was surprised Willis didn't delete it (I thought I had, I guess I left it outside the level parameters). I remember testing EBM's map too, perhaps more intimately than the others. I'm pretty sure his level was the one that wrapped up the crazy minigun guy subplot.