I don't think there really is a great explanation for how Shadowheart came to be in possession of the prism. For games, I'm always willing to do some hand-waving, especially when it's things that set the background of the story. It is however, unfortunate the amount of hand-waving needed for an item such as the prism which sits at the core of plot. In a number of ways, it feels like this arises from some late rewrites and the devs trying to work with what they had - for example, the opening cinematic. I think it would have been fine for the situation of how Shadowheart happened to be in possession of the prism not explained, but then they added the Emperor and also tied it to the prism which presented a number of issues.
If I have time later, I'll go dig through the dialogs to provide better evidence, but for now:
1. I believe the Absolute mentions that it revealed the artefact to the dead three's chosen as it was the sole item capable of thwarting its plans for the Grand Design.
2/3. The Emperor is sent on the mission by Gortash, as the Emperor had been re-enthralled by the Absolute after Gortash discovered the Emperor operating in Baldur's Gate. The Emperor also states that it was just one of many who were sent to retrieve the artefact, the Emperor just happened to be the one to find it first - it's not clear if this means that the Emperor was the first of anyone to find it, or just the first of those sent by Gortash.
Presumably, the artefact would be alongside Vlaakith's phylacteries as one of her most guarded possessions, as it is could undo her reign and prematurely end her aspirations of godhood. Yet, somehow either the (what I presume) stowaway Sharrans or the tadpoled strike team are able to abscond with it. The art book describes Orpheus as being held in an illithid prison, which would have seemingly avoided this conflict with Vlaakith.
4/5. Viconia choosing to send several of her cloister on a suicide mission, including the one person she has spent years grooming to be Shar's chosen is... an interesting choice, especially as she apparently has no idea what the artefact is even used for but believes it can be used against the Absolute. Viconia also states that Sharrans are not adept fighters, but subterfuge is their forte so they would wait for the conflict between the Absolutists and the Githyanki to then steal the artefact. This appears to paint a picture where it seems unlikely the Sharrans would be the first to make contact with the prism - yet, Shadowheart describes her team being cutdown by Githyanki and not the Absolutists. I also assumed that Shadowheart's team used the nautaloid as transportation as there were only five members listed and none of them seemed to have skills for traversing planes, which makes it further questionable why the team would have not waited for the Absolutists to steal the artefact and once it was aboard the ship, steal it from them.
6/7. I try not to include the opening cinematic too much, as changes from EA have created a somewhat confusing situation that is the source of some debate - is the mindflayer we see in the cinematic meant to be the Emperor? In EA, and some surrounding material, it appeared that the garb worn by the Emperor was not unique, and may have been worn as a sort status of rank amongst mindflayers - the ones wearing this garb might have been the Illithid Harvesters who were responsible for tadpoling victims. In the current version, this was changed so that only the Emperor is seen wearing this garb, which presents some potential issues if the devs wanted this to imply that the Emperor was the mindflayer in the cinematic. The Emperor states that upon coming near the artefact, its free will began to return and it decided to go inside the prism to investigate. The Emperor then finds Orpheus and dominates him in order to use his power, needing to establish a dome to prevent the honor guard from interfering once they are aware. Presumably, the Emperor should not have been able to leave the prism once this occurred so if the Emperor found the artefact first, it would seem unlikely that the Emperor was on the ship.
Also, this would be one of those "well, the game couldn't exist then" situations, but it's not really clear why Vlaakith wouldn't just...wish for the prism back? If it's so important to her, surely it would be worth it - she's willing to use up one cast if you say some words that upset her, and it's not like Vlaakith of anyone is at all worried with the price to pay. I'm not really concerned with trying to find every small inconsistency/unanswered question, but again, this is one that popped up due to the change so might as well have some fun with it.
8/9. I didn't interpret it this way, I saw it as stumbling upon additional survivors. In part, due to the somewhat clunky use of long rests to move the story forward, it's likely that you'll encounter at least a couple of them before you even meet the Guardian. I'm not sure if it's different now, but I didn't initially meet my Guardian until the third long rest - long after I had met every origin and had them at camp. How they remain uninfluenced by the Absolute until you find them could be explained by the Emperor proactively extending protection to them. For me, it's one of those handwavey gameplay things that I'm lenient on - sure, it poses some questions but it's not the biggest deal to me. However, it is questionable that the Githyanki were hunting the nautaloid and do not expend a greater effort surrounding the crash site.
10. Presumably, the Absolute is aware of the mission and communicates with the camp. Except, either the Absolute has no idea that we carry the prism, or it is not sharing this information with the camp - Dror Ragzlin uses speak with the dead on the mindflayer if you leave its corpse at the crash site and only then will he be able to learn that we were aboard the ship.
11. This appears to be another "the artefact works however the game needs it to in that moment" or it's part of the Emperor manipulating us, though I don't believe anything suggests that is how the devs intended for it to play out - much like how the other dream sequences involving the Guardian in Act I don't really make much sense. At that point, we should have been protected from the Absolute. We later see that while under the prism's protection, the Absolute is unable to even locate us. Yet, somehow the Absolute was able to not only locate us, but exude enough power to bring us to our knees. Obviously, it makes for a very dramatic scene, which I'm also not going say that I think such things should be excluded as it's ultimately a game, but it certainly doesn't help what comes across as a fairly weak plot line already.
12. This is probably best explained if you choose to believe the Absolute when it states at the end of the game that all of this had been a plot devised by it (whether you believe it could be a debate in itself) - following this, the Absolute needed one of the dead three's chosen to die in order for their hold on it to waiver. The Absolute could have withheld this information from Ketheric so that we would have the opportunity to get close enough and defeat him.
13. Again, this probably hinges on believing that this is all pawns moving as the Absolute predicts - after Ketheric is dead, the Absolute will be able to break free of being dominated and can move onto securing the prism, thus revealing that we are the ones in possession of the prism so that those enthralled by the Absolute can obtain it instead.
Personally, I am not so willing to believe that the Absolute was able to calculate a plan that accounted for so many variables. Especially as if you reach the end of the game, then the Absolute was not correct - somehow able to devise a plot for obtaining the crown, one that involved itself being dominated and ultimately breaking free, and also setting the Emperor free in order to obtain the sole item that could stop it which resides on an entirely different plane and directly inhibits the Absolute's power - just to be dominated or killed by us so close to its goal. Also, prior to being dominated by the crown, the elder brain that would become the Absolute was apparently quite the failure.
Anyway, I don't think this really answers much and probably only adds additional questions. I think that's about as good as it gets regarding a lot of things surrounding the astral prism, though. Trying to use what's in game sort of works for some things, but then always seems to open up additional questions or prevent an issue with something else that might have otherwise seemed answered. A lot of it feels clunkily glued together to try and make those late rewrites work as best as they could, which, seem to work decently enough if you don't question things.
