I'm not sure, but I think David Allen said in one of his books that the Natural Planning Model can be used with various degrees of complexity. If it's a big project involving many people, then each of the steps of the Natural Planning Model can have many sub-steps, and organizing tools can be used to keep track of them. Also the steps are not necessarily done only in order: you can go back and spend time at an earlier step before proceeding, etc. In other words, it can be OK to make something complex and it isn't necessarily over-complicating, if the complexity is useful.
I notice the Natural Planning Model seems to be missing a step: fact-finding and/or agreeing on what the fact are.