For instance, when he listens in on the woman's phone call would that call have happened anyway?
The call is connected just after he starts listening in, which is when the "find employee" objective is completed. It's definitely scripted.
It's the crash that interests me. It's not shown as an objective, are there other ways to get Joe? What about the bystander helping out, and the couple in the car, if there are other ways to get Joe, are there loads of detailed set-pieces scripted into the game? Unlikely, but not impossible. This all but rules out that the crash is a completely unscripted way to get Joe, unless these are mini-scripted events which get repeated at many crashes, or the AI/animation/voice/etc is about 50 years ahead of any other game.
Also, why do they start shooting at our hero? They shouldn't start shooting at any bystander who is covering their face, not in that sort of weather, and they shouldn't be able to recognise him with his face covered. Maybe they're using some hack system of their own, but all to often in games, they seem to use magic, and if you're making a gritty, pseudo-realistic game like this looks to be, that breaks the immersion IMHO.