In Submachine 3 we visit the loop. We are locked inside in the flawless location, at the end we either can finish that final puzzle and drop endlessly to our death, or we can attempt to disconnect from the loop and land somewhere nearby at the lab. However, I feel as if we don't disconnect from the loop, but we disconnect to a false loop. We go from a flawless layer to a flawed layer.
If I misunderstood you wrong, just help me to correct it. It's a lot to wrap my mind around.
Here's my question: Are you saying we jumped Layers all throughout the Series so far? Yes, I know I only quoted the Sub3 bit, but the transition between each Submachine, from your explanation, seems to bounce between Knot locations and Loop locations.
So perhaps this is where your thoughts from a while back about the two Lighthouses fits in: We've thought them to be on different Layers, so perhaps one's a Knot location and the other's a Loop location.
And it makes sense characterizing "knot" and "loop" as "flawless" and "flawed" - A Knot, such as the Gordian Knot, cannot be undone, thus the knot is stable, everything remaining stable within it. Meanwhile, a loop can be undone, being "mutated" and such.
Third dimension. Dimensions are layers. There are seven. So therefore there is a flawed and original copy of the layer existing with said layer.
This was a while back when I said this, but I'm reminded of a thought Vortex and I had: In the way you're saying "third dimension," you're not characterizing Layer 3 as the "third Dimension," which is good. What the thought we had was that the architects layered the Layers in a different order from their creation. So perhaps the fifth Dimension created is "Layer three," being stacked as the third Layer, meaning Layers don't go by chronological order.
If that helps you build upon the Theory in any way, it's there for your use.
Otherwise, I really like this Theory of yours, maybe you could show a diagram to help me out a little more? It sounds like you're saying there's "Layers within Layers," and I'm nearly 100% sure that's not what you mean at all. A diagram might help me make more sense of it.