I just wanted to give an update on this based on my recent experiments. You probably already realized this, but FYI.
I eventually guessed the problem with my take off was that the tile for ww1afg was not flat. So a normal spawn point from the tower put me on the surface, but I believe the Staged Mission logic was spawning me at terrain height which was 30ft below the surface of the square tile geometry.
Since it spawned me underground, the game logic treated that like I had crashed and killed me instantly!
I exported the ww1afg shape and loaded it in AC3D and selected all it's verts and scaled y-axis by 0%. Basically I flattened it. The I re-imported it thru AHObEdit. I also had to modify the standard ww1af tile object because now the hangars were floating 30ft above the new surface.
My new replacement ww1af works perfect now in missions. I can spawn with a taxi waypoint without insta-death.
I can provide it the .ac file if it's useful, but you probably get the point. In any case, that solution works fine for me as I am going to modify and re-arrange the base objects anyway so I'd need to re-build the ww1af tile regardless.
[note] An alternative would be to modify the Staged Mission taxi spawn logic to use the spawnpoint x,z but shoot a hit test vector to find the max y geometry intersect. But since I don't have the source, I had to squash the tile flat. But it looks just fine that way.
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CptTrips