I discovered something odd this week about the bonus chest. I ignored the bonus chest when I started by world. Later on, I decided to move my spawn point 30 blocks higher by building a floating wooden platform directly above the spawn location--part of a larger skybase. So now, when people spawn, they spawn onto a large floating wooden platform 30 blocks off the ground. When I saved the game and re-entered the world, the bonus chest suddenly appeared on my wooden platform in the sky. I certainly was not expecting that.