FWIW, pretty much everything in texmf.cnf can be overridden by envvars of the same name. In Bourne syntax: MKTEXTFM=0; export MKTEXTFM MKTEXPK=0; export MKTEXPK MKTEXMF=0; export MKTEXMF MKTEXFMT=0; export MKTEXFMT (As I recall, nothing enables the other MKTEX* by default.)