During transpeptidation, the acceptor stem peptide terminal D-ala always cleaves. Once this happens the cross-linked stem peptides cannot serve as substrates for d-ala-d-ala carboxypeptidase.
The degree of cross-linking varies between species. Stem peptides that have not been cross-linked serve as substrates for d-ala - d-Ala carboxypeptidase, I can't remember off the top of my head, but I think there are several carboxypeptidases that are responsible for cleaving different segments of the stem peptides during peptidoglycan degradation.
