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I found that when working on my 1979 22' Revenge.........when first purchased all seemed square and aligned. Once I started repairing/retrofitting/customizing not all the angles and moldings true. However, when put together at the factory craftsmen did the assembling to make some of the slight mismatches appear aligned and correct. So, as I have proceeded I found that some of my miter cuts needed to appear square and "reveals" consistent even though my tape measure and miter box said otherwise. I preferred it looking correct than measuring correct. An example would be the wooden rod holders underneath my gunnels. None of the were perfectly exactly alike but the all appeared identical installed.

I wouldn't sweat out slightly off center holes or some slight misalignment's. If the RPS hole alignment for the rod holders really bothered me (and it might very well would) I would wow the holes and center the holders if the rod holders hardware could hide the voids and still be installed structurally.