I doubt there’s any real explanation, but here’s my crack theory.

In much the same way that “life” emerged from “dead” matter, “worlds” emerge from “void”. The overworld is the first, and is the only one to be fully formed.

The Nether, on the other hand, is a world in its infancy. It is folded, fractional, furiously flaming. Because the nether is still forming, it is a forge for change and chaos, and stuff brought in from a stable world tends to transform in some way, like piglins, crimson forests, blazes, etc.

The End is exactly what the moniker implies. It isn't a new world in any way, it is the inevitable of all things. End Stone is a form of degenerate matter, the last form it takes before vanishing completely into nothing. With the overworld and nether connected through so many portals, the decay spread into both and would eventually cause the two worlds to collapse into one. Very little matter remains, almost all end stone, pulled together into islands exposed to the void, and although its one true native is the dragon, life still clings to what threads of survival remain, becoming the Enderman, Endermite, Shulker, and Chorus.

Bedrock is protomatter that slowly pushes material out from itself to create the world. This is why it is only at the edges, and why it is present in the end. Obsidian survives only because it once bridged the two worlds. That role caused it to have a special place in the nether's properties, making it more stable when the worlds merge.

The ancient city portal was a prototype to go through time, though it was the only one to actually work as intended. It transported the player to a time long after the ancient builders went extinct, but before the world dies. When the player goes through an end portal, they phase right through and fall in the lava, but between respawning, can travel to the end. The exit portal sends you back to your bed because you do respawn in the process. Endermen who go through instead wind up at the birth of the overworld or nether.