In configure.ac, lines commented with ‘#’ that occur after AC_INIT will appear in the resulting configure script. dnl comments will not. One purpose of dnl is to discard unwanted newlines in an effort to make the configure script readable. Also, it is appropriate to use dnl comments to document an m4 macro; those comments make no sense in the configure script, since the m4 macro does not appear there, only its expansion.
Comments in Makefile.am are treated differently. Makefile.am is not processed by m4, but by automake, where the convention is to discard lines which begin with ## preceded only by whitespace. (Although ### comments carry through to the Makefile.in) Since Makefile.am is not processed by m4, ‘dnl’ does not introduce a comment.