Shortened abstract: Observations of the nearby Chamaeleon clouds in gamma rays with the Fermi Large Area Telescope and in thermal dust emission with Planck and IRAS have been used with the HI and CO radio data to (i) map the gas column densities in the different phases and at the dark neutral medium (DNM) transition between the HI-bright and CO-bright media; (ii) constrain the CO-to-$H_2$ conversion factor, $X_{CO}$; (iii) probe the dust properties per gas nucleon in each gas phase and spatially across the clouds. We have separated clouds in velocity in HI and CO emission and modelled the 0.4-100 GeV intensity, the dust optical depth at 353 GHz, the thermal radiance of the large grains, and an estimate of the dust extinction empirically corrected for the starlight intensity, $A_{VQ}$. The gamma-ray emissivity spectra confirm that the GeV-TeV cosmic rays uniformly permeate all gas phases up to the CO cores. The dust and cosmic rays reveal large amounts of DNM gas, with comparable spatial distributions and twice as much mass as in the CO-bright clouds. We give constraints on the HI-DNM-CO transitions and CO-dark $H_2$ fractions for separate clouds. The corrected extinction provides the best fit to the total gas traced by the gamma rays, but we find evidence for a rise in $A_{VQ}/N_H$ and a steep rise in opacity, with increasing $N_H$ and $H_2$ fraction, and with decreasing dust temperature. We observe less variations for the specific power of the grains, except for a decline by half in the CO cores. This combined information suggests grain evolution. The gamma rays and dust radiance yield consistent $X_{CO}$ estimates near $0.7times10^{20}$ cm$^{-2}$ (K km/s)$^{-1}$. The other dust tracers yield biased values because of the grain opacity rise in the CO clouds. These results also confirm a factor of 2 difference between $X_{CO}$ estimates at pc and kpc scales.
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