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Downside: you can't do that and weapon mounts at the same time, so weapons will take up normal amounts of space.
You can just assume that the player would have wanted the "massive mount", and build that into your extra-shipsize-mount.
The other way to go is to divide all ship and component sizes by 2. Your cruiser will be 250KT, but shields will only be 20KT, and bridges 5KT, etc.
Then your limit really becomes 128K.