To this day Arma3 AI aircraft choose to fly at a set height above ground level. This is somewhat practical for helicopters however this is not the case with fixed-wing aircraft. it is incredible unlikely that any real life pilot would fly at a fixed level above the ground especially at heights of 500 meters and above, it is simply not practical.
The scripting command "aircraft flyInHeight altitude" will still cause the aircraft to follow the ground pattern.
It would be nice to see a command or simply an in-game option that allows you to set the flight altitude above sea level for an AI aircraft.
Most aircraft have barometric altimeters that can measure altitude from a set reference altitude, mainly sea level.
this is the standard way of telling altitude in an aircraft, always has been.
some aircraft such as Su-25 and KA-50 (that i know of) use both a barometric altimeter and a radar altimeter. the radar altimeter is used to measure altitude above the ground but is rarely used as a reference point for flying height.