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The deck lip cut-out is of no consequence.

It was often done on older boats as a result of shimming the gudgeons to gain more rudder rake (before adustable castings and instead of re-drilling the rudders).
So the rudder pin hole in the fiberglass lip provides no additional lateral stability for the rudder castings? In other words, the gudgeons are doing all the work? Should I shorten the rudder pins then?