IMO, the "cleanout screw" should not ever contact the nipple, and it should not be used as a clean out feature.
The primary reason it is in there is to seal off the drilled hole which connects the nipple with the main charge in the barrel. It is a simple way for the manufacturer to make the gun.
Many rifles with Patent Breeches, don't even have this "clean out screw". Cleaning a gun which doesn't have this screw is not a great chore, and cleaning a rifle without removing it, if it is present, is also not a big deal.
If there is concern about the screw loosening if it's not tightened against the nipple, my suggestion is to screw the nipple in first, put a little Lock Tite on the clean out screw and screw it in until it hits the nipple, then back the screw out 1/4 turn, remove the nipple and let it the gun sit until the Lock-Tite hardens.
Then forget it is even there.
As for the nipple threads that might have been damaged from the "clean out screw" running into them, check them closely.
If they look damaged, or the nipple doesn't screw in easily, by all means, buy a new nipple.
Repeatedly installing and removing the damaged nipple will damage the threads in your guns breech block or drum.
Nipples are cheap. New Breech blocks or drums to replace damaged nipple threads is not. :shocking: