Partly because material thickness may fall between two rivet lengths. It seems that Van's Aircraft is often biased toward the shorter rivet. But variations in manufacturing technique, material thicknesses, etc. can mean that a rivet called out in the plans is actually too short (or, rarely, long) for the actual installation. Perfect technique would be to measure and trim each rivet - yeah, right, thousands of times. In practice, you quickly learn to judge when a rivet is showing enough or too much tail using the Mark I Eyeball.
In the particular spot you were asking about, I found that the called for rivets were just slightly short but acceptable on the brackets and just a bit long but not too hard to drive without tipping them in the other locations so I went with the called out rivets.
