RJ,
From my experience, those gca supplied maintenance manuals would end up being long lost discoveries decades later. Supers change, and almost like new coaches, bring in new people and a new "system." In some ways, if the course doesn't look different, they won't be seen as doing their job. So, they have their own motives to change things a bit, not to mention, many design features just prove difficult to maintain and they take them to some easier level of maintenance, perhaps unknowingly.
TD's example of making knobs rough is a typical one. In general, knobs and bumps are easier to maintain at higher hieghts of cut. And, the "typical" design mode is to use mouds as mowing cues, so if a gca's tendency is to include them in the fw, the second or any subsequent super may not know that and probably doesn't call or consult a maintenance book left behind.
Permitting does take a lot of time in many cases. My agreements have a time limit in the basic fee, and if we get in protracted permitting, extra time is a supplemental service. I have gotten over $100K for permitting on two projects, when $5-10K is standard in the agreement. I think the bigger question is, permitting wise, is whether aerial photography, et all will be extensively used to monitor that courses are maintained in perpetuity to the permitted configurations. I wonder if there will ever come a time when remodels are compared to the original permits to stop them.....
Lastly, Mac has some good points. There are clients, like munis, where the gca is deemed to generally have a conflict of interest - most of us are presumed to want to build a championship course as a monument to our abilities, when the client may very well want a golf factory, or at best, interesting but not difficult pleasant test of golf, especially if the gca hasn't had a new course in a while. It seems odd that building the very best course possible would be against the design brief, but it often is.