It's all in the zones, and mostly in the size of the zones. I'd suggest looking at the applicable zon file, and modifying the Zones.cfg until you can achieve the desired effect.
I'm currently working on a mod to address the propulsion system, correct the location of several zones for equipment, fix equipment labels and repair times, add missing equipment zones, and address bridge/flak/deck gun crew vulnerability (in a way potentially much different than has been tried to date), but it is still very early - though I have been working on it over the past couple of week - and there is much work and testing left to do before I'm even ready to call it a WIP.
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