The 2% - 3% cushion is an attempt to compensate for those that attempt to claim that their motorcycle odometer is accurate. Most of us *know* this is a fallacy. Back in the 'early days' of documenting these endeavors, I suspect there were probably some riders that had to be proven that the bike odometer was inaccurate. Until the proliferation of GPS and mapping technology, that is...
If you say you rode 105 miles from point A to B, but *you* can't *prove* that it's 105 miles between those points, and the cert team thinks it's only 100 miles, seems like it's on the rider to provide the proof acceptable to the cert team that the rider actually rode 105 miles between those points.