Motivated by RIXS experiments on a wide range of complex heavy oxides, including rhenates, osmates, and iridates, we discuss the theory of RIXS for site-localized $t_{2g}$ orbital systems with strong spin-orbit coupling. For such systems, we present exact diagonalization results for the spectrum at different electron fillings, showing that it accesses single-particle and multi-particle excitations. This leads to a simple picture for the energies and intensities of the RIXS spectra in Mott insulators such as double perovskites which feature highly localized electrons, and yields estimates of the spin-orbit coupling and Hunds coupling in correlated $5d$ oxides. We present new higher resolution RIXS data at the Re-L$_3$ edge in Ba$_2$YReO$_6$ which finds a previously unresolved peak splitting, providing further confirmation of our theoretical predictions. Using ab initio electronic structure calculations on Ba$_2$${cal M}$ReO$_6$ (with ${cal M}$=Re, Os, Ir) we show that while the atomic limit yields a reasonable effective Hamiltonian description of the experimental observations, effects such as $t_{2g}$-$e_g$ interactions and hybridization with oxygen are important. Our ab initio estimate for the strength of the intersite exchange coupling shows that, compared to the osmates, the exchange is one or two orders of magnitude weaker in the rhenates and iridates, which may partly explain the suppression of long-range magnetic order in the latter compounds. As a way to interpolate between the site-localized picture and our electronic structure band calculations, we discuss the spin-orbital levels of the ${cal M}$O$_6$ cluster. This suggests a possible role for non-dispersive intra-cluster excitons in Ba$_2$YIrO$_6$ which may lead to a weak breakdown of the atomic $J_{rm eff}=0$ picture and to small magnetic moments.
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