Four main scenes I take this from: the flashback right after the concussion, the flashback when he falls asleep at the control panel, the storm of voices after he regains contact with Ava and she sents him to retrieve the black box, and finally, the ending sequence.

In what I perceive the order of events to go, Simon was born on a planet, not on Eden station. In the storm of voices, we hear his mother saying "c'mon, it has a tree! It'll be just like home. Simon, don't be like that." implying he moved to Eden at an early age.

In the flashback scene with the tree, we see the planets disappearing in real time before their eyes. So, the young actor for Simon is how old he was when the Rapture happened. A fun detail is that in the game no one was actually looking at the planets and stars when they faded, so this is a divergence between the movie and the game, cementing what Szymanski said about them being different continuities.

Shortly after that, Eden Station festered a defeatist death cult, probably because they had the last trees and plants alive. Simon's mother joined in, so he joined in as well, he was just a kid after all, listening to the adults in his life. Then again, I find it interesting that the voices at the end say his mother wouldn't recognize him after he became a killer - then in the same breath say death was all she taught him.

We know Eden has a religious/spiritual motif going on, with that preaching Father, with how Simon calls other Eden people "brothers", how they all get a pendant with a germinating seed, and the tattoo and X/cross motifs that we see across the movie. Simon's tattoo was shaped like an X (you can see where it was burnt off in some parts of the movie), and when he finds the pendant in the terminal, there was a little paper or tape X attached to it and the message.

The tree died at some point, but they said it would live again, because when there is no more soil, their bodies would become the tree's soil. I don't know when this was, but it might have been before little Simon killed all those other kids (or adults? I think they were kids his age). A friend of mine pointed out they were trying to return the universe to nature in the absence of humans, preparing and making way for the plants to come. "Add a little ecofascism as a treat".

Simon, as a child, slaughtered a lot of people in the name of the cult, so much he had the highest body count and was nicknamed "Simon the Butcher". He received a knife and holster from his mother, and he still owns the holster. He keeps it in his vest/shirt, and can be seen rubbing it under his hands for comfort at the start of the movie.

But as Simon grew up, he wanted to escape the cult. He still somewhat agreed with Eden that there was no point in humanity trying to stay alive - given his line to Ava that "Eden didn't delude themselves with hopes for survival if everyone believes enough". But he eventually grew up enough to disagree with the cult. He wanted to live, and he wanted others to live, in his own rebel way.

When Eden invaded Filament Station, he tried to stop it from being destroyed, and in doing so, took all the blame for it. 62 people from Filament died, but none from Eden. He surrendered, no questions asked. He appears as an adult in that flashback of watching the soldier die in fire, indicating it wasn't long ago. Ava was in charge of him as a convict, as we see in the storm of voices scene.

Another difference from the game is that the movie explicitly states Filament Station was destroyed, when in the game it was rendered uninhabitable due to a breach in the reactor core, which, wouldn't you guess it, leaked radiation everywhere.

Some lines he says later on to the Speaker, about everyone blaming him for Filament, give me the idea he still thinks that was his only guilt, or his only blame. He seems in denial of the blame of killing the other kids. Maybe he's repressing it, clinging to an idea of being innocent, or maybe he doesn't think he's to blame when he was manipulated into a cult as a kid?

I find it hard to connect that little butcher to the Simon we know in the movie, someone who even apologized to the control panel of the submarine after he punched it.

"Simon the Butcher, lost his nerve" was told to him by a brother from Eden, whoever the guy who told him to cross the wires was. He implied that after everyone Simon killed as a child, he lost his bravery and devotion to death once he was in Filament Station.

At the end of the movie, I think he puts the knife holster in the life-vest? It was hard to see, so I really am not sure, all I have is someone else's words, who also saw the movie. But at the end there, he does say "oh please, keep this safe, okay mom? It's more than me." Thanks to the good audio, I heard he said mom, there.

Edit after someone commented: he indeed uses the holster to tie the life-vest around the blackbox.

And, that's about the extent I could gather of Simon's past and backstory in movie continuity.

Update: omg y'all thanks so much for the response to this post. I'm really glad I could contribute to you as a lore guide.