In the next development release of ModelConverterX the ground polygon wizard as a new option: Prevent autogen suppresion. When you check this option the file will have the tweak to keep your autogen around the airport. However there is a bug in this tweak that it will result in flickering shadows. So if your shadows are important you better not select this option.
This is just a partial fix of the problem of course, I will continue searching for a few to have both the shadows and the autogen. But at least you have a choice now which feature is more important for your project.