Dealing with "chaos" in consequences-based (fiction first) games

This last decade, the big trend in game design has been the success with consequences that you'll find in system like FU RPG, * PTBA*, FITD and other I forget. A cool feature of the consequences it that it switch from the GM deciding every story point during preparation, in prepping an outline and fill it using the positive and negative "consequences" (e.g. in more classical game you decide that the dagger who killed the king is hidden in the bishop desk, on a fiction first game a partial success may-mean that while you're finding the dagger under the bishop bed, the bishop entre his room an asks you what you're doing.

Now the drawback, is that the whole game-flow can be more chaotic with consequences adding extra steps in the story. I see two difficulties with that kind of approach, one is very practical, making sure that the game session finishes before the last train so everyone can come home the other is finding the balance between staying in your campaign outline, and keeping your plot twist for the right moment, and drowning the PC over tons of consequences. I remember that after a Kult campaign, our GM told us about all the holds (consequences letting the setting do action against the PC) he didn't use to try to stay in the "plot" and not add extra complication to an already complicated story, but the same happen in many "consequences based games).

So out of curiosity, how do you deal with this layer of chaos. Do you go full chaotic, not prep anything and let the consequences driving the history, you limit the dice-roll to not stack up too much consequences for/against the PC ? Or do you adapt on a case by case basis ?