Under the Ocean of the Source (spoilers)

[Enkidoh]

Well there was something under silvertear lake that released a whole bunch of primals, so there is something down there

The general belief for that was that was considerably more recent though - specifically it was an Allagan seal under the lake that kept the Primals in check (remember also the Crystal Tower was still buried there too at that time). Whether that is indeed true though was never confirmed to the best of my knowledge, but is a good a fit as any.

I had a theory when I first finished the initial ARR storyline that maybe the Ascians had manipulated Gaius into deliberately attacking Silvertear for that reason, knowing Midgardsormr would rise up and defend the place, and hoping that the resulting violence between Midgardsormr and the XIVth Legion would be enough to destroy the seal (as to do so required an enormous amount of aether, satisified by the detonation of the cereleum in the Agrius's engines when it crashed into the lake), to allow the Primals to escape (and thus having to avoid needing to create new Primals from scratch when they did their Paragon false-flag operation with the beast tribes).

It all seemed a little too convinent to have all occured by chance (especially in ARR the revelation that Gaius was all chummy with Lahabrea and was clearly being strung along by him), but I admit, as interesting an idea it was, I never really took the theory too seriously.

Now however....