https://forgottenrealms.fandom.com/wiki/NautiloidBy the late 15th century DR, nautiloids had become extremely rare. A few mind flayer colonies still had access to a nautiloid, but kept their existence hidden and only used their ships for evacuation of the elder brain in case of an emergency or rarely during an offensive maneuver, owing to their constant fear of being detected by gith hunting parties. At this time, the illithids had lost the secrets of constructing new nautiloids and did not dare risk losing the few they had left.[2]
In the winter of 1489 DR,[8] the research nautiloid Id Ascendant crashed in southern Icewind Dale near the Spine of the World.[9]
That's maybe the most relevant piece of Lore next to Bada Yaga and Zariel and the Blood War on Avernus.
It's likely Mindflayers have been convinced by someone powerful to undertake that risky research and harvest recon mission to Fearun at all. Mindflayers are a paranoid and cautious bunch by all that is known. Or they divened and targeted sth extremely powerful thaat was temporaily exposed and worth to risk their extremely rare and valuable spelljammer for their survial, protection or revenge.
The Gith encounter hints at this being part of the storyline in Act 1 but all on the highly speculative end with nothing diretly useful to play BG3. It boild down too beware of mindflayer abberations and their allies.
Better make friends with their foes and pile up anything for granting psychic resistance you can find for later use.
But that's plain simple advice by viewing the game trailer as well not to sell those poition for +1 trinkets or waste them on anything trivial.
