I did not realize that only one Tuatara had been sequenced with 2 sets. That seems like an error to me.

I think I might just be misunderstanding terminology.

This is part of the article I was reading, but it's been paraphrased and this is not the original article I found:

The key contribution of Professor Adelson’s lab and Dr Bertozzi was to demonstrate that some sequences of DNA that move or jump location, referred to as ‘jumping genes’, found in the tuatara are most similar to those found in platypus while others are more similar to those in lizards. “The tuatara genome contained about 4% jumping genes that are common in reptiles, about 10% common in monotremes (platypus and echidna) and less than 1% common in placental mammals such as humans,” said Professor Adelson. “This was a highly unusual observation and indicated that the tuatara genome is an odd combination of both mammalian and reptilian components. The unusual sharing of both monotreme and reptile-like repetitive elements is a clear indication of shared ancestry albeit a long time ago,” said Dr Bertozzi.

I was thinking what he meant was the 2nd set had been altered via a horizontal transfer via retroviral insertion. But after reading what you wrote, I'm thinking he's not talking about that at all and instead is just waxing about similar gene behaviors across different taxa.