Maybe the 13th Tribe arrived at Earth in 1947 and crashed in Roswell, New Mexico.
In the 1000 years that followed, they found a way to insert themselves in normal Earth society. They breed with humans. Earth's population eventually becomes a bunch of Human/Cylon hybrids. Some of them (including the Final Five) still know about the other 12 Colonies and develop resurrection technology. The rest happens as we saw it.
Nobody ever said that Earth was empty when the 13th Tribe settled there.