These simulations don't account for human choice on when they want to board. There are customers anxious to get to their seats, and so listen carefully for their zone boarding. There are customers who would rather spend time in the terminal than extra time in an upright seat so they wait until the very last minute to board, regardless of zone.

Increases in prices of checked baggage means many flights have more people carrying bags on, due to limited overhead space, there is more incentive to board as early as possible. If you don't have a carry-on that needs to go in the overhead bins, the incentive to board on-time or early is lower.

Southwest airlines, mentioned here quite a bit, incentives customers to board early (if you want a good seat, you need to get on early to choose it) and to check in early (they can better gauge % checked-in because you are rewarded for confirming with the airline 24 hours in advance). Their policy to allow free checked bags is a nice courtesy but it also means more customer check bags, reducing the time to store things in the overhead which leads to less time at the gate. Free bags is a financial play, just not in terms of additional revenue but as cost savings.