My understanding is:
The question of where we come from? - the Eve Gate, expansion, collapse and re-ascendance - is background information on the evolution of the cluster told for players of the game.
It’s not information that a character in New Eden would be aware of - its the difference between a God like view of the Universe and Humanity’s understanding of how the Universe and Mankind came to be by having measured, observed and generally made up origin stories.
I as a person playing the game have that God-like knowledge, but Terak Romaller - talking to another character in the game doesn’t know that (no character in game does) - so if asked “where did we all come from? why are we all basically identical bipedal mammals?” will put it down as the Amarrian God being the all powerful entity that he is, and that the other Empires are merely those that have yet to be brought back to His Light. He doesn’t know about the Eve Gate being a gateway (it’s a big glowing thing visible from the New Eden system - take the trip there and have a look in game!)
You don’t have to be a Clone to be a neurally enhanced pilot/command system (read “the Jovian Wet Grave”) but there are advantages if you are.
Being Cloned, and having the ability to transfer yourself to another clone isn’t a purely capsuleer trait. But it is expensive. And viewed by some as “wrong”.
The two technologies were developed separately.
The combination of the augmentation and training to use neural interface with the advantages of cloning and the effective immortality that grants, along with the advanced processing and control of becoming at one with the power of a machine is what makes a Capsuleer - and that power and ability terrifies the Empires.
And yes, 99.99…999% of the population are “Baseliners” - un-augmented “normal” people. The differences between their lives and the lives of us Capsuleers is inconceivably vast. You could even say that a Capsuleer has gone way beyond being merely “human”.
Most people will play their capsuleer as more human - mainly because you have to relate to something.
If you are interested in writing fiction in game, keep an eye out for the “New Eden Capsuleer Writing Contest” - I know there will be one this year as well, but this was the advert for last years.