Custom Function 2: 1&2 are Long Exposure NR and High ISO NR respectively.
Do both CF's work in Raw?
1. the Long Exposure NR does affect the raw image,
2. the High ISO NR has no effect on the raw data.
How high an ISO can be used (if any) with say an -3 EV and no ill effects from noise?
The "ill effect" is subjective. On is shooting landscapes in daylight and does not except any perceivable noise in the very dark shadows; another one is shooting a night concert without flash and puts up with lots of noise.
Pros/cons of Long Exposure NR?
1. It slows down shooting (it creates a black frame with the same shutter time),
2. it creates "black holes" (literally).
You can do the same with your own black frame shot immediately then and there and substracting that in PS, under manual control.