Kota and Onsen aren't really brothers in a mortal/human sense. They're two beings created through the splitting of a river deity. There isn't really a, say, biological component to it. They're brothers in the sense they have the same progenitor. But they didn't share a womb or anything.
Lots of myth from virtually every culture works this way, or in even wilder ones. The nordic god Kvasir was born after a bunch of other gods chewed berries, spit into a cup, and mixed their spit together. Aphrodite spawned from the cut-off testicles of the titan Uranus, and that isn't even close to the strangest birth in Greek myth.
They're just... different. They aren't siblings in the same way we would be.