The governing equations and effective boundary conditions to describe thermal vibrational convection in a near-critical fluid are derived with the help of the multiple-scale method and averaging procedure. In contrast to Part 1, this paper focuses on the effects of density non-homogeneities caused not by external heating but by vibrational and gravity stratifications due to the divergent mechanical compressibility of near-critical media. It is shown that vibrations generate non-homogeneities in the average temperature, which result in the onset of thermal convection even under isothermal boundary conditions. An agreement with the results of previous numerical and asymptotical analyses and with experiments is found.