The more I think about it, the more I realize that Perlman's narration of the "Independent" Vegas is pretty much BS in 99.9% of the cases, because the player him/herself will determine its outcome. Yes-Man might be the interface, but the player runs the show, and he/she will determine the outcome.
For instance, as a friend to the NCR, it is highly unlikely that I would require the NCR to leave the Mojave. I would allow them to retain McCarren, Helios, and the dam, as long as I got the 5% of the power output I wanted. And, I would explain to them that the Followers were not to be interfered with under any circumstances, and that they were to leave Hiden Valley and Red Rock Canyon alone. Additionally, I would offer terms of alliance if the Legion were to return. And of course, I would try to find a way to deprive House of direct control without killing/totally isolating him; he might be an arrogant SOB, but he's a genius and a visionary, and such a man would be an invaluable asset. In many instances, though, the game forces you to do things that you might normally not do.
Would this work? I think so. After all, the general consensus is that if house wins, his hundreds of Mark II Securitrons are so powerful, he can take all of their territory from them, and wrest total control of the dam as well, and destroy their economy by charging exorbitant rates for water and power, all without fear of either military or economic reprisal. Offered far more generous terms, I think that the NCR would gladly fall into line.
House could have written his own deal to support NCR annexation, but it was never in the cards as he never had any intention of negotiating with the NCR. Joining the NCR would mean having to talk to other people who weren't subject to his will....which would bruise his massive ego. His plan all along was to get the NCR to protect him from the Legion until he could retrieve the chip and activate his Securitron Army then dispose of the NCR once they drove back the Legion. Then once in control of the Dam economically exploit the NCR for all it was worth. Without killing him or unplugging him (which to him is worse than being killed, there is no Yes-Man ending as the Lucky 38 network controls the Securitrons and House would much rather be dead than have anyone hold power over him. If you leave him in the network he will find a way to get control back and then do whatever he has to do to kill you. As far as the NCR, either you have a Securitron Army and don't need NCR troops, or you destroyed the Dam's generating equipment and there is no reason for NCR to be in the Mojave in the first place....they probably wouldn't annex the Mojave if you begged them to at that point. They aren't going to spend money and the lives of thier citizens to make you richer, they went down that road with House already. And without cheap power from the Dam....how long will the Strip continue to be a tourist magnet? The likely next step for the NCR would be to either have some of the deep pockets in the NCR set up thier own version of Vegas in the NCR proper or sink lots of caps into Primm as keeping I-15 clear from Mojave Station to Primm wouldn't be that onerous and with I-15 north of Primm being either left to the Powder Gangers and/or the BoS why would tourists go to the Strip?
If I were the Courier and going Yes-Man, I would be imposing some sort of order as otherwise there is no point in booting the NCR to begin with. I have no interest in being a fascist cosplayer like Caesar or a Robber Baron who conducts business at the point of a gun like House....but I'm not just going to sit there while the whole region is plunged into chaos when I have the power to do something about it. Going Yes Man to bring about "Anarchy in the Mojave" makes no sense....the Courier would do it to take charge of thier own destiny and impose his/her own Order or create the conditions for the people to decide that themselves.