Not every event that can be somewhat compared has to be 1:1. I see what he's saying. Khans are people of the wasteland, NCR is fast government growth that absorbs anything in their path and has to squash or assimilate any locals in the way. Saying they both came from the Vaults is kinda pointless as if that was always something we had to ask about, any allusion to this idea would be moot since there aren't foreigners coming to the US in Fallout to colonize it.
Yes, in this case the Khans do reprehensible shit like raids and pillaging and drug trade. The NCR though, is still evil in a different manner to many, many people of the wastes. Even the innocents. Look at how Easy Pete feels about them within a few minutes of playing New Vegas.