TEPaul,
The retainer method allows the architect to see the "will of the membership" more clearly, versus the want of the current green committee, Chairman or President.
It is a more lasting relationship, a film, rather than a frame, that allows the architect to clarify his mission over time.
If The last green committee brought in their man for a Master Plan, the current green committee might reject the plan, and bring in another architect for yet another plan.
Tom Doak's position brings continuity, tenure and stability to the process, usually resulting in a better product for the club.
However, some clubs want to alter their great architecture in the name of the most current fads. Just look at all the disfiguring of great courses over the last 50 years.