Yeah for the first part of the fight, the TD will intentionally interrupt your chain. I don't know if its a based on health, number of turns or w/e but eventually it will actually start to help you complete the chain for the CC. Only way I've ever been able to get it off on it.
In terms why you don't see that in games much, has to do with the fact that many players felt alienated when they went through the whole game, defeated the TD, and got treated to nothing... I know I was pissed until I found out that, that wasn't the real ending.