Every implementation of Dynamics NAV is completely different from another one. The reason is because every company, no matter how similar of industry, is run differently. The company that is going to use the ERP software (usually called the customer) is different, the requirements are different, the scope is different, and even the team implementing it might be different. This brings a lot of uncertainty to the process and is the main reason why methodology has to be used.
Implementing Dynamics NAV is considered as working in a project environment. By definition, a project is a temporary endeavor undertaken to meet unique goals. The company implementing Dynamics NAV (usually called the consultant) is probably used to this kind of environment. On the other hand, the customer is probably used to working in an operational environment, where the same processes are repeated over and over. For the customer, implementing a new ERP system is like running in the jungle with dozens of options...