[Coldsaturn]

I have nothing to add, your notes are immaculate.

Actually I have something to add, but your summary IS crystal clear.

- "exposure to the Deepspace Tunnel apparently warps or removes memories with long term exposure. this is presented as a fact and a reason for the drug."
Ok hear me out: what if that's not actually the case. We know that the toring chip is a mandatory procedure and not everyone is happy to comply. So what if the info that the deepspace tunnel causes the very same symptoms that people who have the chip exhibit is just a front to blame something else and even make the use of certain drugs necessary?

- "Caleb takes about three days to regain most of his core memories"
If we buy into the loss of memory to begin with.
When Lucius is being briefed on the problem with Caleb's brainwashing, the dialogue states "However we can't access the chip's records of Caleb's memories." Caleb's memories. Not "part of his memories"
So we can take it in the romantic way and think that Caleb has only managed to seal off his memories of MC, so that no matter what happens he'll always remember her, or that the entire section of his brain dedicated to his memories is off limits to Lucius. Which would mean that when the chip detects an emotional overdrive and sends a reset zap, he will lose consciousness but won't have his memories wiped out.
So I don't know if Caleb actually lost his memories here, or if he only pretended he did to test what MC would do (similarly to how he let her search his computer).

- "Text indicates that memories formed after chip implantation will be wiped when the chip is lost"
It's also very interesting that MC does not lose her memories of what happened while she had the chip. Possibly because the implantation was so short it didn't have time to cause damage.

- "Is he trying to tell her that nothing can ever be lost because there is always the ultimate restart? Or is it meta-textual fuckery by the devs?"
I think your "together or nothing" is very accurate for Caleb. I don't think he knows they can reincarnate, I think he genuinely thinks he can fly her to another planet where it's just the two of them and they're safe (very convenient that he's a deepspace pilot in a place of power), and if things go to shit, we have already seen from the Decoherence trailer what they're both ready to do.

- "each of the "boyfriends" is actually just one soulbound/soul, split into fragments and traveling through time with her"
This is a delightful theory, one that could potentially work with canon in surprisingly fitting ways.
Fandom-wise it would be a disaster because it would "solve" the otome part by integrating all the LIs into a single love interest, making all the fans who only vibe with one guy (to the point of hating the others) absolutely lose it. But narratively it makes sense in ways I cannot yet share openly with you, not until you go through World Underneath and Death&Rebirth.