Because many of the trains on the Santa Fe route are loaded in Southern California with imported containers, those trains are normally full. In fact, they tend to be pure double-high containers and then either pure pigs or racks. That is, there are very few "holes" in the air flow. I read that the fuel efficiency is not affected by air turbulence unless the air gap is more than 12 feet.
But it is evidently higher priority to avoid an empty car than it is to avoid holes in the air flow. This would explain why I had seen a car that had a half-length trailer at the beginning of each of the units on the CB&Q route. Another example was a Santa Fe route train that started out "text book"---5 engines, BNSF 7906(ES44DC), 4361(Dash 9-44CW), 7544(ES44DC), 4143(Dash 9-44CW), 6640(ES44C4), followed by a bunch of double-high stacks.
And then a bunch of pigs.
After quite a few pigs, they started putting containers on some of the trailer cars to keep weight on the trucks even though it is less efficient to put a container on a flat car than in a deep-well car.
And near the end of the train, they had a couple of holes. The first half-length trailer would weigh down the leading trucks. The regular trailer would weigh down the articulated trucks, and the second half-length trailer would weigh down the rear trucks.
In contrast, the modular trains on the old Burlington route are a mix of stacks and pigs including single containers in deep well cars. They evidently keep adding blocks of modular traffic to the end of the train as it goes across the country. And they tend to use a lot more single-unit, instead of 3-pack, container cars. So they don't try to load the train for aerodynamic efficiency.
The car loading evidence that an empty car is too light to be stable at high speed explains why I saw a train of nothing but empty container cars going eastbound through Macomb, IL, on June 13, 2014. So if you do have to run a train slow because of an empty car, then take as many empties as you can. And by not putting any loads on the train, you are not slowing up the delivery of those loads because the train has to go slow because of some empty cars.
Union Pacific is experimenting with an Arrowedge®.
Update: On June 19, 2014, I caught two westbound modular trains on the CB&Q route. The first was pure stacks and most of the units were double stacks. The second started with a lot of trailer traffic and then had some container traffic mixed in. So westbound trains that are loaded by the Cicero yard are much more aerodynamic than eastbound trains going to that yard.