i'm in your conscience
One might wonder that about buildings in real life though. Some buildings are just overly complicated and have secret doors and all this crazy stuff inside. Oh...which makes me think, since you brought up items...don't have an answer for those OoT temples BUT. I think that in Arbiter's Grounds, perhaps it belonged to a secret society. Only this secret society was given the Spinners so that they could get through their headquarters and intruders could not. Though, imagine Arbiter's Grounds fixed up some more haha. I imagine that by the time Link gets there, it's been there several hundred years and has had its fair share of wear and tear haha.
As for Bongo Bongo, I assume his soul was restless and his spirit lives on in the form of...a penis with hands. lol That's just what I think though, hence why he's still there in that shadow form and the other form that Link fights.
Bzzzzzzzt talking about temples makes me excited to finish my RNG project since it's Zelda related. Hopefully y'all will like it. XD