Using the quasi-classical kinetic theory of dielectric relaxation, in addition to existing methods, fundamental mathematical expressions are built, which make it possible to more strictly consider the effects of the main charge carriers’ (protons’) tunneling on the numerical values of the molecular parameters (activation energy, equilibrium concentration) of protons in HBC. The formulas for calculating the statistically averaged non-stationary quantum transparency of a parabolic potential barrier for protons have been modernized by more stringent consideration of the effects of corrections caused by an external electric field. For the model of a double-symmetric potential well, a generalized nonlinear solution of the quasi-classical kinetic equation of dielectric relaxation in HBC was built. The phenomenological Bucci-Rive formula for thermally stimulated depolarization current density (TSDC) was first investigated, taking into account quantum transparency, for the case of a parabolic potential barrier. The choice of the parabolic shape of the potential barrier allowed, at a theoretical level, for the mathematical model of relaxation polarization to be brought closer to the conditions of the real spatial structure of the crystal potential field, in comparison with the rectangular potential barrier model. It has been found that quantum effects due to proton tunnel transitions significantly affect the mechanism of thermally stimulated depolarization currents in HBC, over a wide temperature range (50–550 K) and external field parameters (0.1–1 MV/m). Generalized solutions of the nonlinear kinetic equation, recorded considering the effects of field parameters on proton tunnel transitions, made it possible to significantly approximate the theoretical values of activation energies, equilibrium concentrations of protons and amplitudes of the theoretical maxima of the current density of thermally stimulated depolarization, according to their experimental values in the field of low-temperature (50–100 K) and high-temperature (350–550 K) maxima of TSDC density in HBC. For the first time, precision measurements of TSDC temperature spectra were carried out for chalcanthite crystals. The effects of alloying impurities concentrations and crystal calcination temperatures on the parameters of experimental maxima in the TSDC spectrum of chalcanthite were established. A physical mechanism of the quantum tunnel motion of protons in HBC with a complex crystal structure (crystalline hydrates, layered silicates, ferroelectric HBC (KDP, DKDP)) is described. The patterns found in this article indicate a fairly high degree of applied scientific significance for the obtained theoretical results, allowing for the further development of electrophysics and optoelectronics of heterogeneous structures (MIS, MSM) based on proton semiconductors and dielectrics (PSD) and their composites.