At present, grep-files-aliases suggests "[Mm]akefile*" when you start rgrep in a Makefile.am, which is not at all what one usually wants, as it greps through long generated files.
I suggest the following pattern, to go just before the Makefile entry:
("am" . "Makefile.am GNUmakefile *.mk")
Makefile.am catches automake makefiles, GNUmakefile is often also used for GNU-specific hackery (e.g. by gnulib), and *.mk catches other GNU-ery such as gnulib's