I tend to regard Nyx and Kybele not as two names for the same Goddess, but as two distinct types of Mother Goddess. Whether “Kybele = Rhea”, I really am not sure, but I know that those who dismiss Kybele’s cult as “foreign” carefully don’t mention that Rhea’s cult is of Minoan origin. There’s also the fact that in Boeotia, Kybele in specific was regarded as a wife or consort of Pan — and if getting a Husband Whose cult can be traced to the Hellenic mainland is good enough to make the Kypriot Aphrodite “Hellenic enough”… Really, some people are major weiners about this, when it’s all really quite logical.
My comprehension of Kybele is also a tad outside the modern “Hellenic mainstream”, and (at least based on what I’ve s-far concluded in my studies of Boeotian traditions), probably closer to an ancient Boeotian understanding — if not a perfect match to Boeotian thought (at least for some poleis), then close enough to be likely accepted, should I finally get that phone booth back in working order. 
I don’t see Kybele as a match to Rhea, but Gaia, though I honour Gaia and Kybele differently. Let’s compare this Goddess to a a sort of Borg-like entity — They are distinct, but clearly share a consciousness. Where Gaia is the literal Earth, and a living organism, and a Goddess, She’s also rather impersonal1 — this is where Her Kybele form is necessary and also a distinct form for Her consciousness. As Pindar reports of Thebes, I too see Her as a mate of Pan.
As much as Kybele is a nurturing and deeply feeling Mother Goddess, one Who will cuddle you into Her many bosoms, She will sit you down and tell you very frankly what it is. She’s a Goddess of opposites — She’s both a physical and spiritual being, She’s a Goddess of wild things (and indeed, mated with a god of wild things) but Her crown is a city’s walls, and (perhaps most tellingly) Her mythos tell the story of the first surgical “correction” of an Intersex infant because a few gods were offended and disgusted. 
In part for Her origin mythos, and in part for the story of Attis, Her son, going mad and ritually castrating Himself, Her cult, in ancient times, maintained a priest/ess caste of biological men who willingly submitted to a ritual castration and adoption of feminine identities (and, in modern times, this is often interpreted as having been a haven for trans women and male-assigned genderqueer people — but this is a modern Anglocentric culture’s interpretation, I know of nothing that survives of writings from this priestly caste that articulates their own gender identities), which has given Kybele a special reverence to many transgender and intersex individuals. Unlike Eros, Hermes, and many other Trickster deities, She doesn’t exist in the liminal, in-between spaces — she simultaneously exists on both sides of a divide. Like all mothers, She can be both your greatest ally and worst enemy.
Many modern Pagans and Polytheist have this ridiculously romanticised vision of “nature” and the “natural world”. 
This idea that an untamed forest is a place of kindness, that the planet will just “give” everything needed to Herself and the creatures that live on Her surface. They forget that Gaia throws tantrums — or, if those fits are acknowledged, it’s always with the adage that “we humans deserve it” — forgetting the ill impact these fits have on other living things. While Gaia tends to eventually sort out Her droughts, and blights, and hurricane devatstations, these events still have impacts on plant life, animal life, human life, and even Her own face. It seems only logical to me that Gaia and Kybele are the same soul — They’re clearly a Goddess of opposites.
Nyx, too, is a Mother Goddess, but also not. She’s the mother of Eros, a creative force, mother of Eris, The Oneroi, the Moirai, Furies and so many other Daimones, but this is not a mother Goddess as we mortals understand the concept.
Queen Alexandra (1844–1925) — widow of Edward VII and mother of George V.
That said, I obviously lack a personal relationship or deeper understanding of Nyx — and unless Eros changes His mind, I won’t need to know any time soon. She’s His mother, via parthenogenesis — She was born with his zygote already inside Her when She and Erebos were formed from Khaos. She’s a Deity that all other Deities hold in great esteem. She inspires the occasional mortal burst of insight to Her nature. That’s good enough for now.
1: But as with all polytheist topics, your mileage may vary.
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