Catalyzes the initial reaction in intramitochondrial fatty acid synthesis, by activating malonate and methylmalonate, but not acetate, into their respective CoA thioester (PubMed:21841779, PubMed:21846720). May have some preference toward very-long-chain substrates (PubMed:17762044). {ECO:0000269|PubMed:17762044, ECO:0000269|PubMed:21841779, ECO:0000269|PubMed:21846720}. This is the function of ACSF3 (acyl-CoA synthetase family member 3, Ensembl gene identifier ENSG00000176715).