It's possible that Gortash might have thought that the Moonrise alterations to the tadpole might allow the Absolute's influence to remain in the proximity to the Prism, even if the standard Mindflayer brainwashing would fail.
Of course, this is predicated on some pretty weird things. Such as not figuring that the whole alteration of "Tadpole doesn't completely eradicate the infected's entire brain" would mean that of course it would be a dumb idea to put any such person near the Prism. Surely if they know enough about illithid to make the alterations they'd know that it's likely that the tadpole would be supressed enough that the persons actual brain could take over again...
Then again, we see that It and the other Mindflayer on the ship (The one fighting Commander Fiery Greatsword) are seemingly unaffected by the Prism's proximity - Both consider you to be thralls due to having a tadpole in your brain, indicating that they haven't had their Mindflayeriness suppressed (The Mindflayer is also able to kill Commander Fiery Greatsword... Also you as well when he figures you're not a Thrall because you didn't get to the controls like he ordered so it's not like his powers are being suppressed by the Prism either)
Mephistopheles involvement is suspect... For sure the indications are that he is because of the ability for Gortash and Durge to make it out of Cania with an item of importance. But we have something similar with Shar in regards to how Ketheric and Balthazaar managed to use a ritual to bind Dame Aylin to Ketheric within Shadowfall without Shar doing anything about it. (Also, how is Orpheus' honour guard able to portal their way into and out of the Prism at will? Given it's supposed to be a prison created by those who are against Orpheus, why is it so easy for them to traverse it while the people who made it can't even find the bloody thing when it's right under their noses?)
As such, it comes across as more of a "We really didn't think these lore points through very hard" situation.
I think, the mindflayer on the bridge is not affected, because Empy is already in teh Prism and controlling it. We know, that he is able to decide, to whom he gives protection( like seen with Minsc), so I would say, that is not totally out there.
I agree, that Gortash didn't think that through or he would have at least included some non tadpoled people to help, in case, something goes wrong.
About Shar: I think, Ketheric boundAylin to his life force, when he still was Shars champion. I think, this was the reason, Balthasar couldn't enter the Shadowfell anymore by himself and had to rely on the group. But I agree, that Shar should be more upset about all that.
