Same implants, new parameters.
The One is an anomaly that repeatedly emerges from the system. Yes, the machines may have designed that specific field fetus to become the vessel of that anomaly, but I don't think that's the case. Instead, their problem is that any connected human could become the One. This time around, it ended up being Thomas Anderson, but it could have been anyone else, including Bane.Neo could have been given a non-standard port in the clone tanks, but how and why would Bane have one
So all ports get hidden features to drive the One back to the Source.
No, I think he was referring to the transition that just happened. The one that then let Neo see the yellow code of the Source and stop sentinels.