The Comment by [Jefferts et al. PRA] discusses the microwave lensing frequency shift's possible dependence on the initial wave packet size and two effects of wall interactions, the frequency shifts that they produce and the nature of how dressed states are clipped by apertures. I identify conceptual errors in their criticisms, some of which are related to fundamental problems in their lensing treatment [Ashby et al. Phys. Rev. A 91, 033624 (2015)] for the NIST-F1 and F2 atomic clocks. Aside from typesetting errors that they note, the criticisms in the Comment are shown to be incorrect.