I'm no scenery designer, but after watching a few SDK tutorials, I've successfully added several 'rectangles' that exclude default buildings. It's removed the generic structure engulfing the terminal and after playing around with rectangle heights, also managed to exclude some generic buildings around the helicopter and Milford Sound hangers.
Not ideal, but it's gone all quiet from INI here...
This leads me to wonder if in the process of fixing the runway bump, either (a) it's altered the height of the terrain which seems to affect exclusion rectangles; or (b) these exclusions have been deleted.
In any case, be great to have access to download v1.0.2 again.