make[2]: Entering directory `/var/tmp/portage/xfce-base/xfconf-9999/work/xfconf-9999/common'
  GEN    xfconf-marshal.c
  GEN    stamp-xfconf-marshal.h
  GEN    xfconf-alias.h
/bin/sh: ./make-exo-alias.pl: Permission denied

caused by the fact that $(PERL) is empty, because of this:
if test "x$use_perl" != "xno"; then
    AC_PATH_PROGS([PERL], [perl5.8 perl5.6 perl5 perl])

the same call is required if maintainer mode is used.