Scattering spectra from radiative non-Hermitian systems often exhibit intricate line shapes, where peaks typically garner the most attention for mode identification. However, in multimode systems, the valleys between these peaks may contain valuable information. This "coupling" feature arises from the nonorthogonality of modes in both far and near fields, giving rise to diverse and complex spectra-hole-burning (SHB) patterns. Traditionally, the interpretation of these SHBs has focused on Rabi splitting or Fano resonances, often concentrating solely on either far-field interference or near-field coupling. However, it is essential to recognize that both phenomena coexist in non-Hermitian scatterings. In this study, we develop a quantitative quantum model to probe scattering SHB by simultaneously extracting near-field coupling rates between system quasinormal modes, nonradiative decay rates into a heat reservoir, and radiative decay rates into a vacuum reservoir for far-field interference. We apply our model to illustrate the concept of geometric engineering in tuning the ratio of far-field interference and near-field coupling, exemplified by a silver dimer transitioning from cube-dimer to sphere-dimer or cubedimer to nanocube-on-mirror configurations. Through this, we establish a universal design guideline for non-Hermitian scattering by creating a two-mode SHB library based on arbitrarily tunable far-field interference and near-field coupling. The developed model serves as a generalized diagnostic tool for probing the SHB mechanisms in all types of non-Hermitian scattering problems, promising to advance our understanding of intricate phenomena and facilitate the design of tailored optical devices with enhanced performance and functionality.