Unfortunately, If I can recall, the only time we really go on the lower levels is on the NCR and Legion endings, and they win in their own respective endings by default, so there's no definitive answer as to the outcome of the battles in the lower levels, but since the NCR reaches the Legate's camp in the Inde and House endings and Oliver gives pretty much the same speech as in the NCR one about how satisfying it is to see the Legion rout, It dosen't look good for them.
Btw, I had a much different impression during my playthroughs. It just so happens I didn't feel like I had to play the hero in order for the NCR to win, and the NPCs around me more or less cleaned house on the NCR ending, particularly in the turbine area at the very bottom level where all the rangers spawn. The only reason I had to fight at all is because the Legion troops don't spawn until you get close enough on the map. The only thing that I saw as indicating a 'lack of prepardness' was the occasional line of frantic pvssyr over the Emergency Radio broadcast (although one of them turned out to be an 'Aliens' reference), but then again, the opening moments of any major battle is always chaotic, and it seems unreasonable to conclude that they were disorganized.
And in regards to your last paragraph, I would suggest you look up the concept of "Interior LInes". The NCR's main problem in the Mojave is its distance (and that distance complicates their logistics), and the Legion's relative proximity to the theatre of battle (meaning their supply lines are much shorter). If the Legion were to take the Mojave, and that's a big, big *if* right there, as there is little historical precedent for a preindustrial military conducting a successful conventional invasion of an industrial power, their roles would be reversed, as the Legion struggles to maintain its increasingly long, vulnerable supply lines in territory with hostile populations while the NCR continues to enjoy all the advantages a defender has, particularly when said defender has a massive advantage in firepower. A Legion invasion of the NCR would only get harder, not easier, the farther they get.
Frankly, in the short-term, neither side has shown the capability to bring about a decisive and total victory, with the NCR currently facing steep, but transitory problems at home (the BoS war and the resulting economic damage) while the Legion is hardly equipped to invade a much more modern country well in their own turf due to systemic problems rooted deep within their country (their relatively primative state.) If tribal, preindustrial armies, even ones with (some) modern firearms could have conquered the industrial West, they would have, and today North America today would be carved up into several separate nations by the various native american tribes. But that's not how history turned out, did it?
The NCR ultimately won at Hoover Dam before you betray them with Yes Man/House because you hamstring the attack by either killing Lanius or forcing him to flee.
You clear the command camp out by yourself (and your followers)
So..... Longknife's point still stands.