You conclude that you had to retain disbelief vs. suspending it. Retaining is a constant act of volition. Hence, it nags at the mind and spoils the experience. As a screenwriter/creator, you must feel an especially strong irritation at this, for you have a better idea as to why this is happening and how it could have been prevented or ameliorated.

Two, you write, “It is clear that some if not all of the elements and creatures can be taken as a form of symbol or metaphor. . . . Yet, the questions were and are simply too big to be ignored.”

Perhaps that was this overreaching director’s Big Mistake. He intended to make a symbolic microcosm of human experience first, and stretched a veneer of horror-fantasy story elements over it second. He ought to have gotten his world nailed down first (that is, get the story and its rules down) and then, where possible, tweaked in some social commentary.

Kubrick shows the way. He has said that the story, first and foremost, drives the process. That’s one reason why he took so long between films–a truly terrific story is not easy to lay hands on!