I don't think it said that the Leviathan had been there for a billion years, only that the Leviathan itself was a billion years old. The Leviathan is definitely a Reaper and it appears to be different from the usual giant metal cuttlefish, so a proto-Reaper could be an explanation. It could also be that they just retconned it into a regular Reaper and it isn't actually different at all.