We compare estimates of the empirical transfer function (ETF) to the plane SH-wave theoretical transfer function (TTF) within a laterally constant medium for invasive and noninvasive estimates of the seismic shear-wave slownesses at 13 Kiban-Kyoshin network stations throughout Japan. The difference between the ETF and either of the TTFs is substantially larger than the difference between the two TTFs computed from different estimates of the seismic properties. We show that the plane SH-wave TTF through a laterally homogeneous medium at vertical incidence inadequately models observed amplifications at most sites for both slowness estimates, obtained via downhole measurements and the spectral analysis of surface waves. Strategies to improve the predictions can be separated into two broad categories: improving the measurement of soil properties and improving the theory that maps the 1D soil profile onto spectral amplification. Using an example site where the 1D plane SH-wave formulation poorly predicts the ETF, we find a more satisfactory fit to the ETF by modeling the full wavefield and incorporating spatially correlated variability of the seismic properties. We conclude that our ability to model the observed site response transfer function is limited largely by the assumptions of the theoretical formulation rather than the uncertainty of the soil property estimates.