{solved}
I've experienced issues with 2D skyboxes in which I've been able to see through the back of nodraw textures when looking through the skybox. The only way I found the circumvent this was to use linked_portal_doors separating the two areas, putting the one with the skybox-textured walls/roof above the rest of the map.
I don't know if this will necessarily work for your condition, but try it anyway.
tldr
skyboxes should be in places that are unreachable. so if your skybox comes down a wall to an area you walk near, this is a mistake... either cover that wall with some other texture, or have some door close, and manually close an areaportal on the visleaf showing the area
I think what he is saying is that he wants the player to be able to "walk around in" the skybox which is not visible from the rest of the map and he wants it to appear that it is NOT a skybox while the player is inside it.
The best way to prevent the regular level geometry from showing through the skybox is to put something between the two areas that is textured black on the side facing the skybox. This will cause the skybox to appear solid even though the engine does not consider it solid. You will in essence see black through the skybox and since the engine does not render black over the skybox, you won't have the "transparent sky" problem. It also can depend on the sky texture the skybox is using.
You have no idea how confused this is making me. Im just going to branch off into part 5 of this mappack and eliminate an entire map to see beyond the room textured for a 3d skybox. So that kills 2 birds with 1 stone.
And I have to note for the 100th time, It makes no damn sense that a sky camera doesn't directly project from where itself is located in the map. They should expand on its flexibility by making it work similarily to the point_camera and monitor somehow
The thing is that its position is compared to the origin of the map.
The camera registers the stuff that's around him. It needs to know what the area is where he's projecting from.
It might look like it might have been useful if you could just place the position from where it would project but in the end it would still have the same effect: You need a reference geometry with the sky camera fixed in the position from where it projects. The only thing it'll do is add an extra entity...
mindnumbing madness this programming stuff is
It can be confusing. Just take it slowly and don't over think it.
too bad you can't preview something to it's exact rendered detail before compiling
If you have a scaled down replica of your main map in your 3d-skybox you can see if your 3d-skybox matches up with your normal world geometry. The best way to make sure you don't mix your geometry and skybox it's best to put the scaled down world geometry in a custom visgroup 
im doing something where there is no sky to speak of. You will see when the time comes 