re: the story. seems like some sort of israel/palestine conflict. the birds get pushed from their ancestral home by teh ghosts/ninja and get killed for trying to leave their designated area. however i think this is totally coincidental. the gold orbs are video games.
also i promise that the ninja did not always have that music. it was added in an update and was substantially louder than all the other music. matt also added special hard mode music in that update (also too loud).
also some of those fake walls you pointed out are totally bullshit lol. however--the undertomb one at least has a Lore Book that says it exists somewhere on the beach or whatever.