They abandon Primm because they can't defend it from the Securitron army, but they don't abandon the Mojave entirely, I think they fall back to the Mojave Outpost.

So you count the small outpost on the edge of the Mojave as significant territory?

Not significant, but it's still their territory.

^^^^That's not what that says. Contrary, that's what I stated: The NCR abandons most of their positions throughout the Mojave. They do not fully leave the Mojave, which is supported by the Independent ending slides.

This^. "Small territory" does not equal "no territory".

Just 98 percent of it

The bottom left corner of the map used to be old California, so the NCR wouldn't be kicked off the in-game map entirely, just the parts that used to be in Nevada. Primm was always technically on the Nevada side of the line, but Nipton is still de jure California (for what that's worth with the state it's in) and they'd have the Mojave outpost. So in the Independence ending the NCR aren't kicked out of the Mojave per se since the Mojave desert crosses the border between old Nevada and California, however New Nevada does claim the vast majority of the in game map.

You aren't labelled as a terrorist in an independent run are you

Neither are you in a Legion run

^^ No, only in a Legion run.

Well I was wrong

The Independent path will trigger it upon the completion of either Wild Card: Change in Management or Wild Card: Side Bets, then fail upon the completion of the other.

Caesar's Legion will trigger it after the third part of Render Unto Caesar, and fail it after the fourth.

Its both independent and legion