Just realized something...
I tried to test a different mission with the same kind of setup.
When I "Play Mission" from the mission builder, the AI shows up where the spawn "stationary aircraft" is, and end up doing what Alpha mentioned in the initial post. But when I load up the mission as if I'm hosting a coop, the AI aircraft all show up where they're supposed to (on the runway).
THIS is not good, as I'm sure all mission builders realize that to "test fly" a mission will result in all of the AI spawning where humans were meant to spawn, and not on the runway, causing chaos.
The only work around I can think of is to build your mission.. test whatever you're going to test, and when you figure it's ready for consumption, you could begin setting the spawn points. Either that, or test the mission as if you're hosting, but that means you can't use time compression.
Too add, the test I did was with a flight of four and this works as well as the the test mission I posted above.