A few ideas off the top of my head: Sastasha NM took place while the Garleans were still in control of Castrum Occidens, a base whose purpose was to secure, open, and explore the La Noscean hulk. More wild mobs got into the hulk than bioweapons got out of it. Also, do you recall at which point the Garleans hit an impasse with their exploration? The bottlenecked cave where ADS had set up shop? I assume that ADS did not take kindly to bioweapons attempting to run free. By the time Sastasha HM rolls around, the Imperials have been driven off and the La Noscean hulk has been disabled. Anything not out containment probably died when life-support went down, and everything that was out of containment was able to find freedom unhindered. Perhaps a slither of escaped lamia gained self-awareness and made a break for freedom like their Azys Lla bretheren, taking up a not-enslaved-bioweapon existence in the nearby cave system. Perhaps they had no reason to leave until the hulk's support systems went offline.
Lamia do have an association with water in the franchise.
In FFXI, the Lamia were a beast tribe that were also thought to have origins in chimeric meddling. A subset of the Lamia, the Merrow, had very strong associations with water and were seen as akin to mermaids. Both of these were also known to raise undead (to the point that their army was known as the Undead Swarm), strengthening their connections to what FFXIV would associate with the void.
Captain Morgan doesn't know any more about Allag tech than the average Lominsan. (Probably less.)
Why wouldn't he assume that they were like his crew was?
Nah, I'm just covering all my bases and explaining why I see one given set of ideas as most likely, given what we now as of now.
Even I'm not 100% sure I'm right, lol.
I'm no lamia psychologist, but if they were enslaved weapons for their entire lives, became self-aware, and fled to live in a cave... maybe they didn't want to hurt people, anymore, until this group of adventurers came storming in and put them well under their "kill everything in our path" umbrella. The lamia also say, "There's no going back..." and (something that would be much better for the argument that they were tempered), "One of us! One of us!" (a reference to the 1932 film Freaks parodied by South Park, the Big Bang Theory, the Simpsons, and more). Interestingly, "Don't look at me! Don't look at meee!" was also on the Simpsons.



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