The source of the rumours you've read is very likely Martin Bernal's Black Athena. It's serious scholarly work, but it remains very controversial and, as far as I can tell, current consensus is that he overreached his conclusions. The main idea is that the roots of Greek civilization are not Indo-European but older, connecting them to colonizing Afroasiatic cultures (but as a linguist, I find it utterly indisputable that Greek is an Indo-European language; and I wonder if it would take root so strongly in Greece while leaving intact the culture and myths of an earlier Afroasiatic group and without a substrate layer in the lexicon – lots of native non-European words – to testify for it). In Volume III, Bernal claims the following:

• One Greek tradition says that Athena killed the queen Medusa; there are images of Athena using the Gorgon's head as a weapon (like Perseus) or incorporating her face on her armor.
• There are Athena/Medusa parallels; they both were queens of Libya (as was the original Pallas). Ancient pots found near Knossos, containing children's bones, mixed Gorgon and Athenian symbols (the figure-eight shield). There are also many parallels between Athena, Egyptian Nēit and Canaanite ‘Anat; and the later two have a violent, sacrificial side, which would explain Athena's early association with human sacrifice and monstrous Gorgonic motifs.
• Therefore Medusa is, at the same time, a victim of Athenian sacrifice and an image of her crueller roots. Athena kills Medusa so that she can wear her face.

And it goes on in this note. If you're interested in the question, you'd do well to read Black Athena yourself, and then perhaps some of the criticism (like Black Athena Revisited) and/or Black Athena Writes Back: Martin Bernal Responds to Critics, and so on (there's an entire academic-debate’s worth of books).

/u/sansordhinn has some great observations here. The problem with reconstructing ancient religions is that there are often far too few dots to connect to arrive at a complete picture of what is going on. This is particularly true when peering beyond the "history barrier" into a past just before literacy. We know some things about Greek mythology and Greek belief systems/religions (understanding that mythology does not necessarily equal religion). We also know that people in the Balkans before the Greek language arrived had a belief system (because everyone does). There is the added complication that just because the Greek language arrived, there is no implication, necessarily, of a replacement of culture nor of people. Some Greek speakers may arrived as the language came to dominate what we know as the Greek peninsula, but the new language (and however many of its speakers) encountered an indigenous people with their own culture, language, and belief system. And some of that indigenous culture likely survived, influenced, and blended with Greek culture.

That said, attempting at arriving at an understanding of what that pre-Greek culture and its belief system looked like is a maddening process. There are, simply, too few dots to connect to arrive at a sound understanding of what was there. And when there are too few dots, the point of view of the connector usually has a profound effect on what emerges as a portrait of the past. For several decades, it has been fashionable for a feminist point of view to connect the sparse dots to develop an image of a female trinity of goddesses, and to see a matriarchal society and pantheon of goddesses lurching beneath the patriarchal society of religion of the Greeks. The portrait of the prehistoric bedrock of the Balkans is intriguing and frankly a great deal of fun. The work of Maria Gimbutas was particular important for furnishing a foundation for this line of thinking. But intriguing and fun does not make for reality. My gut tells me that there are some valid strains at the heart of this approach, but I am also certain that it has been taken too far in the name of modern ideology (which is rarely a sound bedrock for good scholarship).

One must also understand that pre-literate belief systems are porous and fluid: that is, they are vulnerable to outside influences and they change quickly, manifesting in different forms from generation to generation, individual to individual, and from one valley to the next. So whatever one could say with certainty about a certain pre-literate culture, would be at best a vague synthesis that would be contradicted by actual work in the field, should one have access to a time machine and be able to travel back to different decades and neighboring places.

In short, if someone asserts that they know exactly what a prehistory belief system was all about, they are almost certainly wrong because nothing in belief systems is exact and there is no reliable ability to assert anything with certainty when dealing with prehistoric traditions.

Question: what is the origin of the idea of multiple-part gods? Are these as common as they seem?

Medusa-Athena, Yahweh-Jesus-Holy Spirit, etc.... This idea of a multi-part god seems to fly in the face of all human experience and just makes these religious ideas even more unbelievable.

Anyway, I know that asking the "origin" is a bit much, but any information or discussion would be interesting to me.

Some of the Individual facts Ive seen are

Homer saying that the Egyptians call Neith , Athena

The discovery of the Minoan Snake Goddess figurines

Early Athena wearing Snakes on her armor ( I know she eventually puts Medusa on it )

and someone even said King Perseus supposedly conquering North Africa ( Im pretty sure the timeline doesnt match up with this one).

and a bunch of the Libyan name for this person is this and that sounds like this or In crete the name for this is that.