Well nuts I thought I was on to something, but I guess it's just a dead end.
The thought was that if all the scripting for the necropolis was inside the background package, then the same thing would hold true for the krypt. But eh, not so much. The idea was to take the loading script that allow you to enter the nekro from there and have it load the alternate one instead. But there aren't any references to bgnd_nekropolis anywhere in the script. There is a nekro_init call in there, but where this function is at is beyond me.
I guess the exe is the next place to look.