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Motivated by several claims of spin-orbit driven spin-liquid physics in hexagonal Ba$_3$Ti$_{3-x}$Ir$_x$O$_9$ hosting Ir2O9 dimers, we report on resonant inelastic x-ray scattering (RIXS) at the Ir L3 edge for different x. We demonstrate that magnetism in Ba$_3$Ti$_{3-x}$Ir$_x$O$_9$ is governed by an unconventional realization of strong disorder, where cation disorder affects the character of the local moments. RIXS interferometry, studying the RIXS intensity over a broad range of transferred momentum q, is ideally suited to assign different excitations to different Ir sites. We find pronounced Ir-Ti site mixing. Both ions are distributed over two crystallographically inequivalent sites, giving rise to a coexistence of quasimolecular singlet states on Ir2O9 dimers and spin-orbit entangled j=1/2 moments of 5d$^5$ Ir$^{4+}$ ions. RIXS reveals different kinds of strong magnetic couplings for different bonding geometries, highlighting the role of cation disorder for the suppression of long-range magnetic order in this family of compounds.