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I think the artifact was kept in Vlaakiths city on the Astral not on Faerun at all. Something that important Vlaakith would want close at hand not in a creche nowhere near her.
Clues from Moonrise towers led me to believe that Gortash (and thus the Absolute) was the main mover and shaker in the theft of the artifact and he certainly had the clout to talk the Sharrans in Baldurs Gate into helping - plus he had a pet Illythid by this time to pilot a stolen Nautiloid- after all the Absolute has a few captured ships and we see them later in Act 3.

So we have a Sharran special forces team on a Nautiloid piloted by Empy which stole the artefact, only one survivor of the Sharrans and shoved into a pod as a 'keep her out of the way so we can get the hell out of here quickly before we double cross the Sharrans' by turning her measure'. So ship is heading to Moonrise. Then Empy discovered the power in the prism and vanished inside it while a few random Illythids which were still on the ship (but had either obeyed the person they believed to be their commander or were controlled by the Absolute to start with) took back control of the ship with no clear idea of what they were supposed to be doing - finding themselves few in number they grabbed a few people from Yartar to replenish their numbers and were in the process of changing them when attacked by the Gith who had probably pursued them across the Astral - Lae'zel actually confirms that Gith chasing a Nautiloid into the hells was unusual so I think at least the higher echelons of Gith knew the prism was on the ship but after the crash had probably searched the wreckage and not found it.

We know time runs differently in the artefact pocket realm so its not inconceivable that Empy had time to sort out the power that was there, at least marginally, to suit himself and thus was able to pop in and out to rescue the party from certain death in the crash. He was after all a fairly accomplished adventurer before he was turned and probably used to thinking fast on his feet (as t'were). It's not that unlikely for that Empy himself organised the attack on Yartar as a way to stop the ship getting to Moonrise safely - something he certainly wouldn't have wanted - it certainly made it easier for the Gith to find the ship and attack it.

She doesn't say this at all but I imagine Lae'zel was caught up in the theft one way or the other - maybe the artefact was kept at HER creche which at least explains why a nautiloid was needed given its on an asteroid. It certainly wasn't on Faerun as there would be no need for a ship to be involved and much less obvious if one wasn't. Or possibly fighters from her creche were the first despatched to get to the nautiloid and get the artefact back which would explain her presence, she may not have known what the objective of the mission was if she wasn't in charge of it and it was organised in a hurry.

I agree Astarion wasn't snatched by the Nautiloid in BG, more likely snatched up by Gortashs folks and transferred to the ship before the theft and kept unconscious while the theft part was ongoing - I would imagine this was entirely a side issue because Gortash wanted to get more dirt on Cazador given he likes to control people and a fairly straightforward way to do that was to turn one of Cazadors apparently loyal followers and its almost certainly the one place that Cazador couldn't enter or send agents to himself, especially if Gortash had a suspicion that Cazador was a Vampire Lord which seems likely.