The physical shape of an organization directly affects how it functions. A flat organization will do business differently than a vertically oriented organization. A company that is geographically diverse will conduct business in a different manner than a company with the employees located in one place.
Seeing the overall shape of the organization and how the parts relate to one another can help you better understand and adjust the processes that make the organization run. The shape and structure of the organization can communicate meaning as well. For example, information may flow with less friction in a flat organization compared to a top-down vertically organized company.
Process is typically thought of as being linear and involves doing one step after another until the task is completed. This may work fine for specific tasks, but not for making an organization operationally effective.
Developing processes without understanding the relationships in an organization is counterproductive. People are inclined to create processes in order to help them define what they don't know.