If you use a silicone RTV, be sure it says it is compatible with aluminum.The more common RTV's like the ones used for bathroom fixtures, tile, etc. give off acetic acid while they are curing.If this is trapped in a aluminum hole, the acid will attack the aluminum. RTV's of this type give off a vinegar smell.Some of the high temperature RTV's sold at many auto supply stores are aluminum safe and should stand a better chance of surviving in that location.
I would just put it on the nuts where they go on the studs. I see no need to put it into the casting holes.
The problem is, even if you welded the nuts to the studs, the studs would still come loose. I need a way to prevent the studs from unscrewing themselves because of the vibration. The studs/nuts could just be replaced with safety wired bolts, but I'm afraid that might put to much stress on the aluminum threads. There is really nothing different here than any other bike, it's just I never saw studs that could be unscrewed by hand before. Most of them are stuck in the head really good.
I've used these on my 3 shovelhead engines since long ago. Solves all exhaust stud problems (& shovels only have ONE stud):