I think the Yes Man ending is better for the NCR than literally siding with them, assuming the courier is open to allying with them. If their farmers get to keep their land around the strip and free transit is allowed to companies like the Crimson Caravan and the Mojave Express, except security is now provided by an endless army of securitrons instead of a massive, bored, slowly degenerating contingent of NCR troops, the NCR is freed up to secure its own borders and prevent any factions like the Legion from becoming a problem again. The only price that would need to be paid is that some of the food from those farms goes to feeding the strip. Plus the strip gets more visitors thanks to trade from the NCR.

Not sure how long that would last considering what happened to the NCR in the TV show, but disregarding that it seems to me like it'd be massively beneficial to both sides.