I have the best results by putting a trigger in front of the a/c with the flyInHeight command there.
The only issue I'm aware of, is that if the flying alt is too high, the game engine doesn't realize the a/c has reached a waypoint, as it seems to go by slant range instead of ground distance.
So if you need an a/c to hit waypoints after setting a high altitute, you must lower the altitude before the next waypoint is encountered. Or just use a script to control the a/c, where you compute the true horizontal distance between a/c and reference location, instead of the slant range.
I've got a GP a/c script that allows you specify an array of locations it should fly through, and the altitude to fly at. It is used in place of waypoints. If you need it let me know and I'll post it.