I'll certainly agree that any limitations need to be presented up front, but I would like to minimize them.
Minimizing or eliminating restrictions on the protagonist tends to make them a nonentity, though. I even put limitations on my players in pen and paper games because I got so effing tired of always having one player who did this:
1. I don't care about this (even if "this" is "I am going to die instantaneously"). I'm just going over here.
2. I don't care about the other PC's and I refuse to interact or cooperate with them in any way.
3. What? No, I'm not sabotaging the game, I'm "just" playing my character.
Yeah, no. That's why I always start my games with this disclaimer:
1. You WILL make a character who has a reason to get involved with the plot. They can resist it, complain about it, whatever you like. But they WILL choose to get involved in SOME capacity.
2. You WILL make a character who has a reason to cooperate with the other PC's. I don't care if they make a lot of NOISE about how they don't want to cooperate as long as you always finagle a way for them to cooperate in the end. That's fine. That's good role-playing.
3. Or, you WILL join someone else's game.
If the only thing that will get you to actually join in this GROUP ACTIVITY is "you have a cortex bomb that will go off if you don't stop acting like an obstructionist douchebag", forget you. Go play with someone else.
That's pen and paper, though. I have no problem if people want to play like that in single-player games, but they need to accept that the result will be "game over, you died".
One option is to have limitations that are based on things that could have always happened AFTER whatever headcanon the player is running. "Okay, so you're role-playing as a person who was summoned across the dimensions to be the Perfect Adventurer. Fine. So we'll leave out any references to your birth, family, and friendships. BUT that doesn't mean that you couldn't have attended the Fighter Academy." Focus less on unchosen stuff like "you were born at" or "here's your bestest friend!" and more on things that don't necessarily interfere with other choices like "you went to school here" or "you got a job here" or "you got shanghai'd aboard this ship" or "someone appeared out of nowhere and gave you this box then ran off".
The trouble with manipulative options per se is that to be *properly* manipulative you have to have a *specific goal*. "Lie and see what happens" is not a goal. The longer-range the goal, the better, because this allows for more possible ways of getting there. You can't really be manipulative if the story (like DA2) is structured in such a way that things happen when they happen. You literally, CANNOT do anything about the Tome of Koslun until the end of Act 2. Even though you KNOW about "The Artifact" quite early in the game, you can't make ANY active effort to go look for it until Izzy basically locates it on her own. Origins at least was more open-ended in this regard. You had a SPECIFIC long-term goal (defeat the Archdemon). You still had few options as to "how" to get there, though. The Landsmeet happened when it happened.