The island itself might be worth only $64 million now. It may have been worth more prior to it becoming infamous, but there is also the infrastructure that was built on the island. That would not have been cheap by any means.
How much was it to build the house and all it’s features. How much to build the airport. How much to build the submarine port?
The $64 million might be a cut in price, but it was originally put up for sale for $125 million. That was probably still a cut from its real value due to its noteriety.
https://www.bbc.com/news/business-60856925
The infrastructure and buildings are included in the price. Even by your estimate it wasn’t anywhere near a billion. I’m inclined to believe Epstein was a government asset, but the island was well within the price range of a wealthy person who wasn’t a billionaire. There are others who also own private islands.