Exclusion rectangles in ADE don't exclude autogen. To exclude autogen, you need an airport background polygon. You can add them in ADE using the polygon tool, choose type Airport Background, and then set the tag depending on the combination of Exclude Autogen, Flatten and Mask Class Map that you want.
SbuilderX can do that too, but if you're just making an AFCAD then ADE can do most of the vector features that you would need.
Not sure about resizing generic buildings. You could try putting multiple buildings of the same type right next to each other instead of stretching them.