[Coldsaturn]

Hell yeeeeeeeah we're going places, finally things are thinging and puzzle pieces are falling. Some of them are falling in the right direction and positions, others are in the correct area, and others are there to trick you into forcing a square into a circle.
But yes, before we get into the thick of theorizing and me trying to support your exploding brain without spoilering anything, can we just comment how absolutely crazy the amount of info that we get in chap 8 is??? It feels like we spend entire chapters in the early part of the section doing nothing but having lunch with Zayne here, taking a stroll with Xavier there, inconveniencing Raf for the heck of it, and little more. It's like 80% filler and 20% plot relevant info. And then you reach chap 8 and they're like "surprise test! hope you memorized every word of the previous 7 chapters, right? Because boy oh boy you're gonna feel lost otherwise"
I'm here to help you avoid too much backtracking (see what I did there?) so you'll save time, but our elders in the fandom had to walk uphill both ways to put all the info together.

Now, before we do anything else, I'm going to ask for your trust and gently push you into doing something: go back to the very beginning of the game, chapter 1. Watch the starting cutscene again.

- Flower shop named Philo, Jeremiah, Xavier (impossible to talk about one without mentioning the others)
The name in honor of their...home planet? So that they can remember it? So that they can feel at home?
Thanks Jeremiah for your service, we would still be in the dark if it were for Xavier and MC's stupid habit of not asking the right questions. So they're a certain kind of immortal. Off the top of my head I'd think about the two biggest versions of immortality we know in fiction: you literally can't die no matter how much someone tries to off you; you won't die of age, but you certainly can be killed by external means. There are a few others that play around the idea of an eternal consciousness more than an eternal body, but we don't know yet if we're in that kind of sci-fi, do we.

- "does Xavier travel on his light, or as light?"
tomayto tomahto. Is his evol a part of his biology or a simple tool that he uses? Some evols collaborate better with the body of their owner than others.

- Jeremiah is "not young"?
Time to possibly confuse you again, because I don't think you're remembering this detail, but Xavier and Jeremiah (and others connected to them) aren't the first instance we find in the game where we are made aware that X person does not show their age. The first we meet is Raymond, that dude you visited with Zayne because he was having hallucinations and then died after acquiring a painting made by Rafayel. Raymond also had something interesting proudly on full display in his big living room.
I'm not saying the two things are the same, but there's only so many instances of people defying the confines of a normal human lifespan before it starts getting suspicious.

- "why do i need a disguise to get into the N109 Zone again?"
It's not an area very fond of Hunters or tourists. If you're there, it's because your hands are dirty at least in some capacity.

- "the voice line went right into my ear at close range"
Needless to say, but this game needs to be listened with headphones because they got the whole stereo thing going on that gets so good in certain parts.

- "Jeremiah walks in...aaaaand immediately walks right back out."
LMAO I love Jeremiah so much. That poor third wheel.

Your theory is definitely in the range of the smoking gun! You got some things right, others are in the general vicinity of the correct answer. Keep piecing things together, you're onto something. 
At this point I'd tell you to start carefully reading whatever Anecdote has been unlocked for you, and if you don't have them yet, then consider working on the affinity with the LIs because their backstory is essential to understand what the hell is going on, since our MC is in the dark. 

- "Non-Intervention Principle", Backtracker, Traceback II 
And the right question: "how long HAVE you guys been here?"
If there's a Traceback II, there must be a Traceback I, right? And yeah, they're here by mistake, and it's a mistake that might just have to be fixed.