I understand these compartment limitations, and I'm not surprised. That's why I'm glad the Liberty Ship is so well suited to vessel modding. I've made about 4 new freighters of about 5000-5500 tons, and there aren't any major zone problems since they have the same basic engines amidships configuration as a Liberty. However, on the Ross/McKnight Class tanker I still need to move the engine room aft. The engine smoke comes from the right location but it just won't feel right if you can immobilize it with a hit to the midships section. I want to move the engines aft but I doubt it's going to be a simple process...
http://visseraa.topcities.com/German/23580140.jpg