Many states require the local parties to pay for their own primaries. Many local parties are bare bones organisations that only ramp up activity every couple of years or so. Voting mechanisms need to be scalable, affordable across a diversity of budgets and technical skill sets. Caucuses, for example, exist because they are dead easy to explain, don't cost any money, and are transparent at least so far as everyone can see who won just by looking around the room.
As far as transparency, that's sort of the main point of the paper: if everyone can themselves check the votes by doing something as simple as looking at something like bc.info, then that imo is a large increase in transparency from the current system which only allows the room-members themselves to verify the results. I agree with you that caucuses in their current form are easy to explain, however I think we can abstract away all the difficult parts and make it a pleasant / easy experience.