Ocean's storytelling style has always been like this. Everything becomes perfectly clear over time, but you don't like this approach to storytelling, it's not that something in the game doesn't make sense. Everything there makes sense and follows the plot.
One of the "mysterious" reasons for the protagonist leaving town was given by Katie directly: she thinks he ran away because of her, they kissed and he, realizing his attraction to her and the possible consequences, decided to run away.
This wouldn't make much sense in a normal situation, in your average college game. But in the circumstanses that Ocean has chosen for his characters, it is obvious. The people the MC lives with are extremely cruel and in some aspects adhere to medieval views and traditions. His act is something like a stable boy kissing a king's daughter who's hand was promised to the son of a neighboring king before she was born. If this comes to light, the engagement is off, the union is broken. And the stable boy will die a slow, painful death.
A mysterious accident - yes, the MC doesn't know what happened to Helen and tries to investigate. He's sure it wasn't an accident and tries to figure out who's behind it. Why this suddenly doesn't make sense?
In order for everything to make sense, you have to believe in some basic parameters of the fictional world. Like in Aliens, if you start denying the existence of creatures with acid instead of blood, arguing that this is impossible - well, damn, dude, why even start watching sci-fi then? Nobody claims that WiAB is a documentary novel written based on the biography of a retired mafia boss.
