The Geneva Convention allows for US waterboarding and worse:
“The Conventions apply to a signatory nation even if the opposing nation is not a signatory, but only if the opposing nation “accepts and applies the provisions” of the Conventions.[12]”
https://en.m.wikipedia.org/wiki/Geneva_Conventions
The US has never ratified Protocol II, therefore we not a Party to that part of the treaty. Your statement applies to how other nations who are Parties to PII should regard us, and it says they are bound by it so long as we accept and apply the provisions. We don't accept or apply the provisions.
In any case, this clause regards signatory countries obligations to us, and not our obligations to terrorists.