I think this is inevitable when you try to abstract and systematise anything. You cant think about big and complex things will all details in mind. You abstract. Same way you don't see a person in front of you as collection of millions cels. You see it as an entity.
The danger is that you end up with a "perfectly spherical cow" that you base your arguments then on, and your abstraction-based results then have no bearing whatsover to the real world.
I'm not saying that you must follow your abstractions blindly. At the end you must always test your theory against reality and adjust if reality contradicts your assumptions.
