Theories by user -NeroZero-BR.
SubWorld Theory (doubtful)
No one knows exactly what -is- the Submachine, what's it's purpose, or how can one escape from it. However, considering a certain number of facts about other theories, The SubWorld Theory is born. Let's start considering facts now.
First Fact: Safe Haven Theory
This theory states that the Submerged Machines were created to protect people from wars and massive natural disasters. The actual Submachine doesn't looks exactly as a "Heaven", but let's consider that it could have been used with those intentions at first.
Second Fact: Amnesia Theory
Basically, every person that enters the Submachine gradually looses his/hers memory, with the apparent exceptions of Liz and Mur. Now, keep in mind that people simply loose their memories from sudden nowhere.
Third Fact: The Edge
The Edge, according to some people, was created to protect the Subnet from -something- at the other side. But, what if the Edge was made only to mark the limit of the Subnet, and that The Edge itself expands as the inner Submachine expands? It's like a medieval fortress: buildings are created in the fortress while having a massive wall limiting the city so it won't grow disorganized. As the number of buildings increase, the wall has to expand in order to let more space in. What if the very same happens to the Submachine, if The Edge expands to avoid confusion about what is and isn't from the Subnet?
Fourth Fact: SNEE
Some people say that some rooms in SNEE were made like to confirm certain theory posted on another room. Considering this as true, and not coincidence, we have the final SubWorld Theory.
Final Theory: The SubWorld
Considering all the facts above, we have the SubWorld Theory. Being based on a certain logic path means it needs a full comprehension of the whole theory. The catch here is, that the Submachine might have been built as an alternative world. An ageless, sizeless, perfect world. With the Safe Haven and Amnesia theories in mind, I believe that the Submachine is a world made for in case of the destruction of the known world, or of a certain civilization, such as the Mayans, that appear with massive influence in the 32 Chambers. My theory about the Amnesia is that it's the factor of the expansion of the SubWorld. I do not know how, but I believe that the Sub drains the memories from people and materialises them as locations, according to the Brain Power theory. This causes the people to go amnesiac while their memories are created as locations. Such as the Mayans, maybe someone with deep study of their age got lost in the Subnet and had all his/hers knowledge about the Mayans converted into the cultural influence showing up in the 32 Chambers. Only a few people seem to be immune or partially immune to this amnesia, which being Mur and Liz. Mur can probably resist the amnesia because of his ability of manipulating passages within the Net, while his memories are "copied" instead of "drained". Such as the Sceptre God that appears in Sub4, that statue might have been made from a moment of madness on Mur's head, where he imagined himself as a god. He also seem to be able to handle a small portion of the Sub, too, since he created, or, at least, used the puzzles at Sub4 that would lead The Player into the part of the Sub that he couldn't control. Liz might be immune to the Amnesia due to the fact of having lived with Mur,even if it was only for a while. Or maybe it's something else that has not showed up yet.
Now, The Edge may have been made to limit the SubWorld from growing at a point that one could not distinguish Subnet from reality, so The Edge expands to avoid creating havoc from randomly scattered locations on spots they shouldn't be. And the Amnesia factor gains strenght by locations such as the Looping Traps, The Ship, The Basement Section at Sub4, The Nazca Room in SNEE, etc. Maybe people with these areas in mind went amnesiac, then their thoughts were made real.
As for the Layers themselves, they are known to be the same thing than a Dimension. So if multiple Dimensions exist, while there is only one copy of every human in each Layer, the most likely reason for such is that these Layers have been created with the sole purpose of holding unlimited amounts of organized contents each, depending on its type - Similar thoughts will be placed in the same Layer.
Crossroad-Storage Theory (doubtful)
A rather simple theory about the Submachine.
Let's consider the fact that the Submachine can bring you to so many places, so many areas... Yet it can kill you with relative ease, if you get lost in there.
But the reason of the great amount of influence of diverse cultures from our current world is yet still unexplained. With this theory, I propose TWO aspects for the existence of such.
1- The Submachine as Geo-Historical Storage
The Sub is not a plain open museum that anyone can visit, but it does contains huge amounts of Mayan, Aztec, Bhuddist and other cultures. While several of these aspects of these cultures are extinct, the Submachine might have been used, at some time, as a massive storage world to preserve the cultural influence of those extinct civilizations. As fdor Bhuddism, this may be due to Liz and Mur, who are seemingly Bhuddist or have some influence from it.
2- The Submachine as Crossroad Between Worlds
Great amounts of influence on a concentrated and specific Location might mean that one is near of an area where such culture's influence is the strongest, which means its origins. So if you arrive at an area loaded with glyphs, statues, Puchs and Bacabs, it might mean that you're near of an Exit leading to the root of the Mayan culture. This might be a dead end, however, since the origins of most extinct civilizations' religions are already gone. The reason of why the Sub passages won't close might be that there is still Mayan influence alive in our World - On the moment that this culture disappears, the passages on the Sub might crumble as well. This might explain the Layers - Each version contains different Cultures, to avoid conflict between them once several have vanished.
Considering both of these aspects might be true, with both supporting eachother - A cultural storage with an exit to its origins. This might explain the Layers and cultural influences.