Noble, but stupid OSS Unit! I tried every darned AI setting I could think of to get it to just "defend the tent like a good chap, will you?" Either the unit would sit passively while the nosy Romanian Military Police proceed to destroy the airstrip, or it would "conquer" the nearby town of Gherghita which in turn would cow the Romanian police unit into its own passivity. Solutions: Change the OSS Unit to human control once its construction task is done and dial up the aggression of the police unit.
Sorry about the multiple Marshalling Yard explosions. I had the bright idea that it would look cool to have wreckage spewing smoke on every turn thereafter (as you know, as soon as any unit enters such a hex, the wreckage is cleared away) so I set it up to re-create the concrete bunkers and destroy them every turn. I did not realize that there would be audible explosions as well, which must have seemed weird and annoying. Removed.
As to "The mission extension should trigger a 'scenario end' condition to allow the player to finish any remaining secondary objectives," I included destroying the rest of the trains along with the fuel depots and oil pumps in the condition for finishing the scenario if that option is chosen.
To aid the airmen on their escape, I have placed small supply caches at a few key intersections along their journey to the woods. (I prefer the airmen as bandits rather than paratroopers for aesthetic reasons and because paratroopers could be used to unrealistically wipe out the Romanian police).
I found the problem with the evacuation trigger. Advanced forensic analysis was necessary!

Ploesti Revisited v1.1 is uploaded.
Changes:
- Returned all Axis AA guns to full strength.
- Provided for the human player to take over control of the OSS Unit.
- Removed multiple Marshalling Yard demolition effects.
- Included trains in the condition for finishing the mission option.
- Placed supply caches to aid airmen on their escape.
- Anchored the "Make a Break" and "Here They Come" messages to the proper spot on the map.
- Fixed an issue with the paratrooper evacuation trigger.