Flying creature combat engagement takes z-axis into account
I'm going to burn at the stake for this, but here we go: The aggro range of Cliff Racers is too small, and by a significant margin.
I believe the main problem is that their aggro range is only 2-dimensional in Morrowind, but 3-dimensional in OpenMW. In Morrowind, they will always aggro if they are within a certain distance around you, no matter how high they fly. In OpenMW, if they fly high enough they will not aggro even when they are directly above you.
Though their 2-dimensional aggro range also feels about 50% larger in Morrowind. When they are on the same height as you, they aggro earlier in Morrowind even though the AI is less responsive. Might need to take a closer look at this.