Did he say anything when you killed the radio tower guy? I've killed the Legion prisoner before but Boone didn't say a word...but it did count as a point. Unfortunately the female NCR glitched and became stuck in that room and I couldn't access her anymore. heh. It would be nice to get 3 points from that one quest chain. I usually go powder-gangers & Cottonwood. It might be nice to be able to put Cottonwood off until later sometimes.
I killed the spy in my first game and that one didn't make the 5 pt requirement because it was early. He killed the spy this game and it was the same. I'm at 3 pts if his kill counts and I think it does because his actions get me bad rep with factions, so why shouldn't it? I just wondered if anyone ran into a problem by letting him kill the spy and it doesn't appear so. No, Boone didn't say anything yet in this game but he got on me when I asked about his wife.
I read about the Boyd glitch if you leave the room when she enters in the middle of the Silus interrogation but I never leave the room. I just stay in there and all is well. I don't get points for that one because I get the info without laying a finger on him so no +1 there; Boone can't always have what he wants.
I also do Booted (Powder Gangers) +2, and Silus Treatment +1 and I do the rescue of the crucified Nelson NCR guys for +2 and I save Cottonwood Cove for later (not worried about the points) after I get the Rebreather because we like to go swimming and wash the desert dust off.
We never pollute the scenery with radiation barrels though...Boone just takes care of business and empties the place out. This time he has backup with Arcade and Veronica and ED-E so it should be even easier.