In "The Hunters', Mac explicitly states that aircraft can't be built. Despite this, the AI can build aircraft
Also the event chain that leads to the player being able to build aircraft doesn't work

I can still not build Sky Factories after the script has fired to enable my engineers to build Sky Factories.
I just played this level from beginning to end. I had zero issues.
The AI is allowed to have aircraft, even if you don't on this level.
Spoiler below:
Just to check, you followed the script by revealing the area noted, dropping in an Incursion team, and removing the enemies buildings in the crater?