Makes sense. But something is definitely off still. Even trying to place mines ~100-200 units behind the Atlas Mk.II engines (where the shield bubble is very close to the model) will place mines all around the Atlas, often 500 units or further away. There is room there but the game thinks otherwise.
This is in contrast to other ships where you can place precision strikes. I.e. behind a Mule, or behind a Prometheus. Right between the engines! With most of the ships, placement very close to the shield bubble is possible.