GDW stopped making statements about deckplans, and DGP decided to ignore the rules altogether.  The "fudge factor" was specific to deckplans, not to construction math.  At least, it was back then.  T5 has a similar approach to construction math, then tells you the effects of going over or under the hull's putative size.

Shattered Ships designs showed every indication of being done with a flawed spreadsheet. I know the work on my private one was ongoing, so the idea that an in-house design spreadsheet might be flawed is not in the least bit surprising.