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In this work, a complementary microstructural and optical approach is used to define processing conditions favorable for the formation of deep boron-related acceptor centers that may provide a pathway for achieving an intermediate band behavior in highly B-doped 3C-SiC. The crystallinity, boron solubility and precipitation mechanisms in sublimation-grown 3C-SiC crystals implanted to 1-3 at.% B concentrations were investigated by STEM. The revealed defect formation and boron precipitation trends upon thermal treatment in the range 1100-2000°C have been cross-correlated with the optical characterization results provided by imaging PL spectroscopy. We discuss optical activity of the implanted B ions in terms of both shallow acceptors and deep D-centers, a complex formed by a boron atom and a carbon vacancy, and associate the observed spectral developments upon annealing with the strong temperature dependence of the D-center formation efficiency, which is further enhanced by the presence of implantation-induced defects.