The guy in the first picture's meant to say something. I'll get around to fixing him in the morning.
As for the other two things, they're more set dressing [the first to accompany that one boss, the second for a place for the implied airship Geaut uses to be stored/serviced at when not in use].
As for the final ending you're missing, it's for when you lose/time out on one of the final bosses. It's there mostly as a worst ending, and so that low-damage teams aren't completely left out in the cold when it comes to that particular final boss.