Weaver himself confirmed that Jay and the white-eyed bird were indeed the same. The idea is that like Ruby and Tom, Jay was also mutating, but perhaps as a result of him being kept within that tank in the Cold Storage room, his manifested more as some kind of psychic ability. The black white-eyed bird was more or less an astral projection that he created in order to try and get help. The “its so dark” was referring to the the tank that he was imprisoned in.
However there are in fact two birds within Ruby Quest. Jay and Ace. Ace obviously isn’t much like a bird anymore, (as seen by his face of worms) but presumably he was before being corrupted. We also know for certain that Ace is the other bird because the Animal Crossing character that he’s based off of, in a similar fashion to the other characters, is also a bird with a spade on his shirt.