One might hypothesise that some or all of the Origin characters were deliberately targeted rather than random victims, and have something the Absolute Spirit-Eater wants to consume.
I rewatched the intro in light of this theory and honestly at this point the intro raises a lot more questions than it answers. To summarize it briefly.
1) Lae'zel and [PoV Character, perhaps Tav] get brain-worms put in.
2) The Nautiloid approaches Baldur's Gate and starts harvesting people from a single street, seemingly at random.
3) The Githyanki hunting-party arrives and starts harassing the Nautiloid.
4) After apparently just the one "harvesting run" across BG, the Nautiloid is forced to jump to some snowy mountainous location.
5) The pond of brain-worms gets blown up and Lae'zel gets loose.
6) Then the Nautiloid is forced to jump again, possibly a mis-jump (as the Mind-Flayer steering gets hit by a blast whilst making the connection), into Avernus.
Then the game starts. So like, this raises a lot of questions about when everyone but Lae'zel was actually picked up. Let's ignore PoV Character as artistic licence, but:
A) Karlach - Presumably picked up in Avernus, but the Nautiloid is already on fire and heavily damaged and being boarded by devils, so it's kind of surprising the Mind-Flayers had the time to worm her up. Not impossible though (assuming there's a second "worm tank", which I think there is).
B) Shadowheart - Seems to have been picked up earlier, which would make sense.
They didn't take her d20 away though so presumably they don't know what it does.
C) Astarion - So he's from Baldur's Gate, but the run through Baldur's Gate is in fairly bright morning daylight. I'd say 6-7am assuming summer (which seems likely from the weather, foliage/trees - it's certainly not winter, autumn, or early spring), Earth-like axial tilt (which the FR has, I believe), and so on, from the long shadows. Seems like he'd definitely want to be long-indoors by then (unless he was planning to "embrace the sun" or something! Being grabbed just before that happened would certainly be A Thing). So him getting picked up is a little surprising. But he doesn't seem like he could be a primary target, given he's kind of the lowliest of the non-Tav characters (despite his attitude).
D) Dark Urge - Only exists if we play them, so presumably cannot be an intentional target, otherwise the weird stuff going on with them would make them likely the reason to come to Baldur's Gate.
E) Gale - Having a massively powerful magical bomb, he might well be the reason to come to Baldur's Gate, so could be the main target.
F) Wyll - Seems unlikely to be intentional, given his backstory, was presumably just in the wrong place at the wrong time.
The other interesting point is that the Nautiloid ship's final teleport is back to a region near Baldur's Gate, which suggests maybe it didn't accomplish its mission, or maybe it did and is trying to deliver its cargo.
