OK, the flap in your second to last picture is an external storage area (albeit a somewhat flimsy looking one). If you're on a long, fireroad climb and feel like losing your helmet for a while, you should be able to unhook the flap, put the helmet on the back of the pack (open side down) and reattach the hooks so you can carry your helmet instead of wear it.
The yellow bag is a "goodie bag." I'm not sure why you'd need such a thing on a MTB but you can throw your dirty clothes and items you find along the trail in there for safe keeping. Given it's bright yellow color, you could also use it for a rescue marker should you ever find yourself lost in the woods.