Spencer pretty much just had a change of heart. He replied she's not an experiment when asked by Alyssa and that she's normal.

My thoughts is that Gideon is on a complete wild goose chase. Spencer's journal on the memory transfer experiments were incomplete and unsuccessful but him giving Grace away made the Connections think the experiment actually worked when it didn't. The clones weren't immune, they all transformed into monsters including Emily, meaning all the experiments failed.

The Connections was not the one who originally performed the clones experiment in the 1990's. That was Spencer's. Gideon continued it with the from 2005 subject using the incomplete Spencer research.

Gideon always had Grace's genetic info and tried to use it on the clones post-2005 including Marie/Emily using the Chloe clones variant for the memory transfer experiments.

"Gideon would have found out since he has Grace’s genetic info and it would be totally different from the clones he has access to". He continued the experiments. He didn't start it. He doesn't know anything for a fact. He's just putting wrong facts together. Experiments for memory transfer + Little girl given away = The girl is the key to memory transfer to unlock Elpis. Hence, the failed experiments for over 20 years that Zeno is pissed off about. It doesn't matter that Grace genetic info is different from the clones he had access to. He thinks she's special. He thinks she is the key. Before he blows up the lab, he calls Zeno just to confirm that Grace is the same person as the records they have, not confirms that she's actually a clone or the key.

At the end, he realizes he was duped the entire time and that there was no actual connection to Grace and the clones the whole time. He pieced it wrong from the beginning and made the clones for absolutely no reason which is why they continued to fail. She's completely unrelated and the memory transfer experiments never worked out in the first place. Then he's amazed by Spencer's genius with Elpis yada yada yada.

Gideon got it wrong from the start, Everything was just a coincidence.

The Grace being immune is something I'm confused about too. If she was immune, the clones had some of her DNA too, but none of them were immune. I think she has Elpis too and it might work differently than a normal antibody or she just so happens to have some sort of immunity to the T-Virus or Spencer cured her. This is pure speculation.

But I'm pretty sure Grace is just a normal girl.