More crack pot theories!
No. A rational approach.

I will be breaking this down into four parts.

Repetition: It's repeated often and thoroughly.
Association: The Ideas are linked to one another by generally appearing with the other.
Opposition: Breaks the pattern, doesn't fit, is a reversal or not the same.
Deviation: Cuts away from the pattern.

Repetition: I cannot believe I saw this more but the game has you going down all of the time. Further in the level? Go down an elevator. Looking at the Core? It's downwards. There was this Guild Hall, and in basic Guild Halls and fully completed ones, you are in a sense of being inside a closed room. Not this one. There was a large casam, going downwards. Most levels even give a feeling of being suspended in air due to the top down perspective, letting you see the Clockworks like a giant cat walk. Always downwards. The Knights even fell from the Skylark, going down.

Association: Now I know that some people might make a point that you are fighting and looking around more then going downwards, but going down leads to the fighting and exploration. Going down leads to the monsters, leads to the bosses, leads to finding Alpha Squad's recordings, leads to figuring out what exactly is going on, and fighting more powerful beings. Go down enough, fight Snarby, a super beefed up Wolver. Go down further, Wolvers develop the dash ability, and then develop the burrow ability, all while getting stronger jaws and hides. The more you go down, the more powerful things become. It's like the opposite of a ranking system, where going up means stronger, going down means stronger here. And the more missions and crafting you do, you find more cryptic clues about Vanaduke, the Gremlins, the Kat Tribe and the Owlites, the Trojans, etc. The deeper you are the more answers you have, especially about Alpha Squad.

Opposition: There's only one case of the pattern being broken. Going up means the Knights can rest and become stronger, which is the opposite of going down and the monsters becoming stronger. Very interesting. No, I'm wrong. You also go down so that you can go up to the stars to go back to your home. And a third case, you get to the bottom of the darkness, the deepest pit of all, the Swarm, and emerge in a Heaven like place. But Heaven is in the sky right? Then why would it be underground? Perhaps its more on the "keep going down" pattern I've been seeing here but I'm not completely sure.

Deviation: The Gremlins, oh the Gremlins. They deviate from the pattern, even though they fit in with the "become stronger and learn more about them as the Knights go down" pattern. They interact with the Clockworks, have the highest sentience of all the creatures in the Clockworks, they all act under orders from King Tinkizar.

Further notes: I am not completely decided on the Swarm, the Arcade, the name "Cradle", the Sanctuary, among other things. I also am too lazy to fully explain how you learn more about each monster family as you go down as well. I am almost certain there are things I missed both in game and in the lore. Also, I used something I learned in school in video games.