ABSTRACTWe present the Rhapsody-C simulations that extend the Rhapsody-G suite of massive galaxy clusters at the $M_{\rm vir}∼ 10^{15}\, {\rm M}_{⊙ }$ scale with cosmological magneto-hydrodynamic zoom-in simulations that include anisotropic thermal conduction, modified supermassive black hole (SMBH) feedback, new SMBH seeding, and the SMBH orbital decay model. These modelling improvements have a dramatic effect on the SMBH growth, star formation, and gas depletion in the proto-clusters. We explore the parameter space of the models and report their effect on both star formation and the thermodynamics of the intracluster medium (ICM) as observed in X-ray and SZ observations. We report that the star formation in proto-clusters is strongly impacted by the choice of the SMBH seeding as well as the orbital decay of SMBHs. The feedback from AGNs is substantially boosted by the SMBH decay; its time evolution and impact range differ noticeably depending on the AGN energy injection scheme used. Compared to a mass-weighted injection whose energy remains confined close to the central SMBHs, a volume-weighted thermal energy deposition allows to heat the ICM out to large radii that severely quenches the star formation in proto-clusters. By flattening out temperature gradients in the ICM, anisotropic thermal conduction can reduce star formation early on but weakens and delays the AGN activity. Despite the dissimilarities found in the stellar and gaseous content of our haloes, the cluster scaling relations we report are surprisingly insensitive to the subresolution models used and are in good agreement with recent observational and numerical studies.