(Spoilers)The rejoining kinda useless.

[QT_Melon]

Though at this point in time we have seen an artificial life be blessed with a new born soul if what I gleaned the whole thing about Alpha correctly, however that happened after the sundering and all the laws were rewritten.

Keep reading. The tale you're reading is his conversation with Hythlodaeus. Which both were suited for office due to their rather unique ability to read the color of souls. Apparently Hythlo was better at it.

Yet like Hades, he was eminently gifted in the ability to behold the Underworld. As a matter of fact, were it purely a question of vision, his was the keener of the two. Precious little escaped his eyes, which could discern essence and appearance as plainly as night and day. This made him amply qualified for the highest office of the Bureau of the Architect

Hythlo had an issue that was apparently happening BEFORE the Final Days where a pheonix or bird was created - which gave you the entry you're reading now.

I have a suspicion that souls joining creation magic may have been the either (and) catalyst for (summoning) Primals/Final Days (may have to do with the sound) idea of summoning a primal to save themselves from it since primals can have "pilots"

Also, why is everyone always stating that the Ancients were immortal beings, where as the shades in Amaurot outright prove that they were very much otherwise?

Because in this case they're talking about their lifespans which are biologically immortal. This is later addressed when Emet in the tales - loses his son to illness when he's in the Garlean Empire.

In the end, they were all just malformed creatures. Feeble, frail, and foolish. Thrashing blindly about in their fleeting, fragmented lives, repeating the same mistakes over and over again. Never could they replace his brethren. Yet in spite of himself, when he cradled the newborn in his arms and stroked that downy hair, he could not help but hope. For what, he could not be certain, but he hoped nonetheless. It made little difference in the end, for his son had succumbed to some absurd illness and returned to the Underworld long before his time. Not without leaving behind a legacy, however─a living, breathing, and ever-present reminder of that momentary lapse.