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.

Oh snap, I didn’t realize this. Yeah, I guess communicating with the local gatebuilder wifi would be standard design for all proto molecule alterations. I guess we see a little of this when he starts being able to read other people’s minds.
In this case he would have started puking and turning into a zombie. Followed by being tossed into a furnace with Cortazar.