I'd like to just add to your point two things. First, this bit of dialogue from the game:
HERMES:"Tell me─do you know the difference between living beings and arcane entities?
It is the presence of a soul. Yet the soul isn't something you can choose to have at will.
No, it manifests only in those beings whose forms adhere to the laws of creation. That can endure on their own.
Beings that do not fulfill this requirement, such as those spontaneously born of magic or natural phenomena, do not have souls.
No matter how much it might resemble flora or fauna, if it lacks a soul, then it is considered an arcane entity.
So you see, it is not for mankind to decide what is living. That domain lies beyond our manipulation, and it is hubris to assume otherwise."
Second, this line from the Through His Eyes sidestory from ShB:
"A soul... How?"
Through their mastery of creation magicks, men could weave anything into existence. Anything they could imagine, they could bring forth─anything, that is, except a soul. As Hades well knew, souls spontaneously manifested within creatures that were born in accordance with the laws of nature. It was a gift from the star itself, long held to be impossible to recreate. No artificial being, no matter how subtly sculpted in the image of nature, could come to possess a soul. Such creations occupied a separate classification known as arcane entities.
Not that I don't agree with your points here, but I'd like to just clarify that unless I'm missing something else that contradicts what we're told here, creations don't spontaneously gain a soul sometimes. In fact, it sounds like it's quite the opposite, that even creatures born of "natural phenomena" sometimes don't have souls (the lightning sprites/pneuma that we see just shortly after Hermes says that, for example).
Which to me, that explains a lot of why the researchers at Elpis seem adamant about testing whether their creations can survive on their own or not, because if your creation can endure on its own and have offspring, those offspring may have a chance of gaining a soul and being considered to be living.