The beginning missions are basically tutorials for overall movement and some of them teach a player how to score higher through the means available (melee kills, combo bonus chests, etc). (gamerstemple.com)
You also get a daily, account bound bonus chest for defeating Tequatl. (dulfy.net)
The vault on Kadara contains a bonus chest that rewards two skill points as well as a chest that can be collected while escaping after initiating the vault purification sequence that restarts the environmental stabilization process. (au.ign.com)