  The SHINING survey (Paper I; Herrera-Camus et al. 2018) offers a great
opportunity to study the properties of the ionized and neutral media of
galaxies from prototypical starbursts and active galactic nuclei (AGN) to
heavily obscured objects. Based on Herschel/PACS observations of the main
far-infrared (FIR) fine-structure lines, in this paper we analyze the physical
mechanisms behind the observed line deficits in galaxies, the apparent offset
of luminous infrared galaxies (LIRGs) from the mass-metallicity relation, and
the scaling relations between [CII] 158 $\mu$m line emission and star formation
rate (SFR). Based on a toy model and the Cloudy code, we conclude that the
increase in the ionization parameter with FIR surface brightness can explain
the observed decrease in the line-to-FIR continuum ratio of galaxies. In the
case of the [CII] line, the increase in the ionization parameter is accompanied
by a reduction in the photoelectric heating efficiency and the inability of the
line to track the increase in the FUV radiation field as galaxies become more
compact and luminous. In the central $\sim$kiloparsec regions of AGN galaxies
we observe a significant increase in the [OI] 63 $\mu$m/[CII] line ratio; the
AGN impact on the line-to-FIR ratios fades on global scales. Based on
extinction-insensitive metallicity measurements of LIRGs we confirm that they
lie below the mass-metallicity relation, but the offset is smaller than those
reported in studies that use optical-based metal abundances. Finally, we
present scaling relations between [CII] emission and SFR in the context of the
main-sequence of star-forming galaxies.
