> We build and build from what we extract from our planet. -- what do we
> extract? metal and stone to make buildings

We extract ore. The most common being Iron Ore. Stone really isn't "extracted."

> Endless complexity in our creations, intrinsically serving to increase
> the level of complexity around both the creations and us. -- we're
> digging to deeply in the wrong directions

I don't think it means wrong direction, just more layers to the puzzle.

> Oh, I'm missing my good friend Sanctus, it seems, but I'm sure he's here
> somewhere. -- something biblical? Not really Bungie style though

Sanctus = Sacturary?

> Too rigid, I suppose, for the level of chaos I prefer. -- mathematics,
> chaos theory (the symbol in glyph 5?)

Too ridge usually means you need to "think outside the box."

> It's like the cat in the box--it won't be determined until you open it.
> There's so much more... -- a reference to Schroedinger's cat, a well
> known quantum physics analogy