David's focus was primarily on getting the runway clear primarily because most people can't get to 10,000 feet because of all the "stuff" on the runway. It's hard to get your airplane off the ground when there are a bunch of huh-stacks all over the runway.
The second challenge is in what David refers to as a project. Anything that has more than one action step is a "project" in GTD and this is confusing because different types of projects need to be handled in different types of ways. In addition the tendancy to schedule actions by context tends to lead to some things being a contextual next action when they really should be part of a more detailed project plan.
Little projects can be done with little/informal planning and will have next actions by context that can be done at odd lots of time. You can call Dr. Jones to set up an appointment any time you have a phone and move your "get teeth cleaned" project forward. Put that call on your @calls list. But if your responsible for "developing comp plan" for your boss (VP of sales) then and you put call boss to discuss success criteria on your @calls list then (imho) you've made a critical mistake. You aren't going to discuss critical success factors with your boss on the project while in line at the grocery store.
The correct approach is to set a meeting with your boss to discuss the project assignment. In fact its probably a good idea to schedule some block time alone to brainstorm what you think the assignment is before you sit down with your boss so your discussion can be as complete as possible.
The focus of GTD is moving projects forward one next action at a time. Unfortunately when taken to extremes, and when we focus solely on the runway, it is all to easy to move lots of projects forward without ever completing any of them. It takes the discipline of the higher altitudes to say no to projects that aren't in alignment with those altitudes and further it takes discipline to limit your current projects list to the critical few so that they recieve enough focus and attention that you do more than move them forward, but actually complete them. There are several references to this sort of thinking in David's materials, but unfortunately, there is so much focus on runway activity, that this kind of stuff is often missed.
In short, focus on the big rocks; move the little things forward through the cracks in the rocks; and leave yourself enough time to enjoy life in the process. This requires strong decision muscles, and the ability to say no.
Examining ones thinking is always good. I don't think you are off-base. I think you are dealing with some grad-level GTD issues... Unfortunately to date, we only have the undergrad textbook...