Catalyzes the elongation of long-chain fatty acyl-CoA with 3 or 4 methylmalonyl-CoA (not malonyl-CoA) as the elongating agent to form tri- or tetramethylated-branched fatty acids known as mycocerosyl lipids. 3 (R)-methylmalonyl-CoA + 9 H(+) + long-chain fatty acyl-[mycocerosate synthase] + 6 NADPH = 3 CO2 + 3 CoA + 3 H2O + 6 NADP(+) + trimethylated-mycocerosoyl-[mycocerosate synthase] 4 (R)-methylmalonyl-CoA + 12 H(+) + long-chain fatty acyl-[mycocerosate synthase] + 8 NADPH = 4 CO2 + 4 CoA + 4 H2O + 8 NADP(+) + tetramethylated-mycocerosoyl-[mycocerosate synthase] Binds 1 phosphopantetheine covalently. Homodimer whose monomers probably have a head to tail arrangement.