How did protomolecule break containment to alter Duarte?

At the beginning of Persepolis Rising Cortazar explains that the human stem cells injected into Duarte were altered by the proto molecule. I'm guessing they then removed the proto-molecule from the stem cells before injecting them into Duarte. This was to mimic the drone repairs on Laconia.

My question is: How did the proto molecule defeat this big constraint and mind control Duarte? Cortazar was explicitly removing it from the stem cells. The molecule could only "perfect" the stem cells in regard to efficiencies the ring builders knew of. But by Leviathan falls they definitely have full control of Duarte anyways.