Hi Paul, I would look at it not as a 'what is programmed and what is not' approach because ultimately knowing it doesn't make a difference really. Everything you currently are and all the fears or desires you have are yourself, doesn't ultimately matter if pre-programmed or self-created through habit or societal influence. The point of this whole process is to learn how to work with the aspects that you see in common sense are detrimental for you and so establishing the ways to create new living skills and habits that are supportive.
So, common sense: if holding your breath is NOT supportive then, you have to focus on normal breathing since that is just part of how our bodies operate, it's not about going for or against what we are 'programmed' to do because a program is not wrong or bad, not even preprogramming. It's all about learning to take direction within our lives and that means getting to know yourself to decide what do I see is necessary to change in order to get to live a life that is supportive? Doesn't matter how big or small the aspect of yourself you are looking at, because it's all self-created ultimately - whether preprogrammed or not.
So, to make it simple, I would recommend not going pondering what is preprogrammed and what isn't. But simply focus on the writing to identify that which you see you have to change and use the tools to lay out the foundation of how to practically in real time change, which is what really matters in this whole process of self-awareness and change.