Some measurements (I don't remember which) even seem to have shoe height built into the measure. We had measured DD at the doctor's office in October and she was a hair or two over 42" barefoot. I had them measure twice to be sure so we wouldn't be disappointed at WDW in January. When we got to WDW, she measured too short for a ride with a 42" requirement. I know she didn't shrink, so my conclusion was that they assumed "tennis shoe" height for January and built it into the stick - she had been too short in flat sandals on a warm day. She got on later in the week wearing her usual sneakers. Remember she had been over 42" barefoot as measured twice at the doctor's...
We have also been asked to remove shoes to measure a "questionable" height, so in addition to safety issues, you could get "caught" wearing extra height. That being said, we did once wear thicker than normal soles in hopes of getting on Space Mountain because the restraint would actually fit shorter DD who had some meat on her bones better than tall DS who was too skinny for the bar to keep him from sliding around... Really, if DH and I (over)analyze it, we come to the conclusion that some of the industry's attempts to make ride restraints "idiot proof" have actually made them less effective! ...but that's another topic...