The AI system (even for FS9) is still a black-box kind of problem where experimentation is all we have in the absence of any real information. For example, AI arrivals will sometimes use runways marked as closed for landing even when there's a parallel runway available, eg Heathrow, where I use the southern runway for departures only, but have seen a BA 767 arrive on it all the same even though it is closed for arrivals at both ends.
You cannot close a runway completely in FS9 or FSX. What you can do is lower the runway score card so another runway is prefered. AFCAD was not designed to lower the scoring of a runway in FS9. The closing checkmarks are a holdover from FS2002 where a one end of a runway could be closed.
All this changed when FS9 was released. In order to lower the runway score you have to remove all associated approach code for that runway. AFCAD or any airport utility that mimics AFCAD cannot do that.
FS will never leave a IFR FP airplane in the sky. They always must land. It does not matter if the only runway available is 1000 ft long with no approach code a B747 on a IFR FP in zero visibility will land on that short runway.
Also I'm not sure my experience agrees with your assertion that arriving AI are allocated a parking place prior to reaching a hold-short node after exiting the runway.
The parking spot is allocated when the AI Plane reaches the taxi in segment of the flight. There are 4 segments to an arrival AI Plane.
Enroute
Landing
Rollout
Taxi In
Taxi In occurs when the AI Plane slows to 20 kt IAS while on the runway. At this point the parking spot is assigned. It has nothing to do with the holdshort node. The arrival holdshort node has one purpose and that is for switching to ground freq. If no hold short exist then planes stack up at the parking spot based on the sort list of parking that FS uses.
With regard to the tutorial, you mention that AI uses black links in the shortest route to the threshold, but that's not universally true.
I agree. Only the first plane in the takeoff and landing sort list will normally use the shortest route. When a airport fills with takeoff and landings ATC does its best to avoid taxi stalls between airplanes. You will see AI planes exit runways in opposite directions and take longer taxiway routes to avoid other AI Planes that are taxing out to a runway. It is for the reason the plumbing system does not work for all airports.
The plumbing system is trial and error. There is no such thing as a oneway taxiway in FS. It might appear that AI Planes taxi on a oneway link but when airports get conjested (on the ground) AI Planes will taxi across grass to bridge a taxiway link. At that point it does not matter which way the taxiway is set for the parking spot.
The plumbing system must be tailored for each individual airport and that is not a guarantee that it will work correctly. The Flightplans for my AI Planes may be from one developer and yours may be from someone else. That also plays a part on what your plumbed airport may do vs your airport using my FP's.
I have downloaded developers airports that use the plumbing system. In their testing it worked. Once my Flightplans were used for that same airport the plumbing system falls apart. The end result is each user must tweak the plumbing based on how their airport is used. The larger the airport the less likely the plumbing system will work. Try plumbing KORD or EHAM with all runways active. Major caios.
In FS9 the turnout parking works well
In FSX the pushback parking limit works well.