Solid skies are a bug in older map compilers. Maps with solid skies needs to be fully recompiled. 

One concern I have for moving the origin point of nails is, if it's too far forward it might spawn outside of the player bounding box, and you could have exploits where you can shoot through a thin wall or similar problems. 

I might even remove those skybox fixes from my code again if they don't do anything. Then again... why did they put them into the URQP, then?

But I think it was just about the grenades. They used a trick to delete them when touching the sky and then respawning them again at the right place and time, if I understood correctly.

Anyway, this isn't the most important feature to have. Btw, even in the Quake Re-Release it only works in ID1 and SoA, but not DoE. They didn't touch those maps, which is also why they don't have fog or light effects (not even transparent water, I believe). 

I believe the DoE map sources were lost so there wasn't much they couid do, unfortunately. 

To fix that you can do a short traceline in front of the player before spawning a shot, to check if there's something between the player's bbox and the spawn point, and adjust the distance accordingly if necessary. It's what I did in Alkaline and worked perfectly 

nice... I was also thinking you could spawn an invisible (null model) nail and then set it's model after a short amount of time.