I can give some information from the perspective of a software developer on a SCRUM or AGILE project. During the course of an iteration I'm assigned one or more stories. Each of those active stories goes on my Projects list at that time. The remaining stay in the master project backlog (not a part of my system). My action lists contain at least one next action (bookmark) related to each story (project).
The GTD system is meant to be a simple system that holds the reminders of outcomes you've committed to finishing at various levels and the next action that you would take to move each one foreward. It's not a project management tool like MS Project. Complex project plans are regarded as support materials to be utilized during reviews to decide intermediate outcomes and actions at any given point in time.
Does that make sense?
That makes sense, and it just like keep say, "play guitar" on my trusted system instead of writing each note down in it.