But the system just doesn't make sense.
You are meant to be in conflict by undertaking a course of action. Except if that action has positive consequences you aren't. So if you rob from the rich to give to the poor your conscience, in game terms, will be crystal clear and you will only ever gain morality.
That makes no sense. You are meant to be in Conflict, you are a person acting in a period of turmoil. The mechanic woudl seem to imply that you have to make difficult choices, except it doesn't because if you choose to steal something you only get Conflict if you do something that isn't, by nature, conflicted. If you choose to steal from the poor, for instance, you earn Conflict. But all you've done is just...steal from the poor. Where is the conflict there? All that's happened is you've behaved like a tool.
It does seem as through they wanted something like Mass Effect's moral system, but the problem is that in video games being the bad guy just means being a **** while the majority of the gameplay favours being the good guy.
What should happen, if you are going to have a system of points for Conflict, is that any negative action should earn Conflict, no matter what the reasons are or the outcome. But that would make the game rather tedious because the focus won't be on the adventure or the characters it will be on the GM adjudicating the morality of every action they take. The only way Conflict can actually BE conflicting is when the character does something that is otherwise immoral because he thinks its going to achieve the greater good. But in the rulebook such actions expressly do not garner Conflict points.
Even so, if the system were to change the consequence of Conflict is random. So you are playing in a game where you will get points for how you behave buit it's out of your control what happens as a consequence: you might become a better person, or you might not.
I don't think this has been thought through very well.