43.13-2B, as I was made ABUNDANTLY aware from AEG, is only applicable to UNPRESSURIZED aircraft UNDER 12,500 pounds, so make sure you "fit" into this category (please read the bitterness in this...long story), but I agree with RB that it is probably a company guideline or a justifyable engineering judgement.
Determine the max clearance between the pin and the hole, misalign the pin by that much and work the geometry. For inline loads, I've seen a Fitting Factor of 1.15 generally applied.