Actually, I got the feeling that it's all done using the game engine, just some bits are choreographed. Yeah, the part where they're forming the square isn't great, but it certainly doesn't look any worse than the formation shifts in the older games. It seems to me that you're approaching this wrong. You're comparing it to an average game trailer, when what you're actually looking at is close-ups of Total War units. It's nothing like the Shogun 2 trailer, which was entirely pre-rendered.
