The rules are good, but far from perfect. Once a departure is made from their standard box, penalties are imposed to bring one back to that box. This usually results in very heavy scantlings and out of proportion material sizes for different parts of the hull, such as the rudderposts, stems, keels, etc. Most will consider modifications to their rules if elaborate mathematical proofs are proffered and even then will probably class the vessel as experimental. There is also a cost factor involved for certification and plans approval, which may be justified on multiple buildings when it can be prorated, but is often beyond the budget of the individual owner.
Most designers have their own scantling systems based on each family of vessel they design.
For example the scantlings of a steel dory are quite different from a steel sharpie, however, both are different than, say, a trawler, although all may be of the same length and breadth and, in the instance of the dory and sharpie, may also be of the same depth. This is a simple example that one rule cannot fit all vessels without numerous exceptions. Some designs may need slightly heavier plating due to their occupation and expected maintenance. Others can use a smaller corrosion factor, thus lighter plating. The designer from experience and observation gains a sense of what is good, acceptable, and bad.