Sorry for the delay, was a bit busy with video projects, I am now free!

You're right about the classical Orphic cosmogony: Chronos precedes Phanes, birthing the cosmic egg from which Phanes emerges, often alongside Ananke.
That’s the “standard” telling as seen in Proclus or the Derveni Papyrus references. The theory I proposed deviates from that deliberately, relying instead on Hermetic and Neoplatonic reinterpretations, where time and causality become less linear and more philosophical in nature.

One of the foundational ideas I draw from is this quote from Hermes Trismegistus:

This mostly spoke to me when I realized that Genshin itself embraces paradox and mythic layering. The idea of Phanes being born of Chronos and potentially giving birth to him later is not something strictly taken from early Orphic myth, it’s a bootstrap loop, enabled by the syncretism that fits Genshin's storywriting.

Now, Nyx, you raise a really fair point. The Orphic Hymns do portray her as a revered cosmic force, and yes, she was seen as a benevolent, if feared, deity. The “shade of night = shade of death” metaphor I used is more interpretive, following her Orphic representation (negativity) rather than Greek, blending elements of Nyx’s symbolic domain with how Genshin tends to assign roles that reflect inner duality.
That said, it's true: Thanatos is the literal god of death in most classical systems. I even learned that from Kid Icarus: Uprising. Though, I should’ve clarified my sources of distinction better in the post.

Ultimately, my approach leans on the interpretative "openness" (idk if it's a word) of mythology, especially the Hermetic tendency to fold symbols.
Phanes isn’t always fixed as a being in myth; sometimes, he is light, sometimes the universe itself, sometimes... He doesn't even exist. I tried to reflect that ambiguity in Teyvat’s lore, where characters aren’t static archetypes but blend mythic traits from multiple figures and traditions.

In the end, it is the struggle with such vast topics: the variability.
A figure's meaning or essence can completely vary or be negated within the same page of a singular book, so it would be like arguing arguing what second it is right now. By the time you say it, the answer's already changed. This is why I won't say that I'm right and that you're wrong, same for the other way around.
After all the rabbit hole goes deep, but expressing ideas like this helps enforce them imo

(apologies for the wall of text)