There are a few things I think have better references here (but this is my opinion):Layer 1 - Seems simple, like The Basement.
Layer 2 - A stairwell leading to a mostly empty room, I think it's reminscient of The Lighthouse in that aspect.
Layer 3 - Leaves, trees, like the leaf in The Loop? A casual reference?
Layer 4 - Now we visited The Lighthouse again in Sub5, but the sewer systems of the Lighthouse.
Layer 5 - The Ancient Section of Sub4?
Layer 6 - A primal "DefSys" ("The Armory.")
Layer 7 - The Core, signs of a(n ancient) civilization.
Layer 1: The Basement? I don't see much of a connection. Somewhere the void would be visible would have a stronger connection. Either that or Liz's ship (green receivers and green karma portal).
Layer 3: That leaf is not native to The Loop. (Wait, what if Layer 3 was the source of the leaf in The Loop?) The winter palace seems more suitable since it also has trees.
Layer 4: Maybe. How about the sewer-like place on Liz's ship that has the Karma portal to the Secret Location?
Layer 7: could you clarify?
I'm confused, where did the engine come from?"The engine"