differences happen when you try to mesh to intrinsically different mechanics and styles. Its a little like translating a sentence from one language to another. translation differences creep in.
as stand alone games both systems work well within their own frameworks. The designers at Gurps may have different priorities when creating their version, and may have different interpretations of various fine details.
Unless all the various groups got together and worked out a uniform method of handling various facets of ship construction. As well as adopting a universal list of priorities, requirements, and methods, no two versions are going to be 100% interchangeable.
Of course for various reasons that is about as likely as a snowball vacationing in the lowest level of certain underworlds.
unless there is money, life, limb, or the survival of mankind involved, in many cases about the best way to handle the inter system discrepancies is to issue a wiggle room writ...
In this case the exact tonnage required for a J-6 system in a 100 ton hull would require the vessel be right around 110 tons.... that's inside a 10% variance limit, so I'd say close enough.
