Matthew.
As a member of the ASCE 7, 41 and AISC Specs Committee, I would agree with your reflection that these modifiers are not applicable to moder, prequalified connections. However, you may wish to review the criteria in the newly issued AISC 342 Specification available for free download from AISC (for professional members). This Specification "Seismic Provisions for Evaluation and Retrofit of Steel Buildings" substantially updates the AISC 41 criteria and presents AISC's recommendations for nonlinear analysis of steel structures.