In the mailing lists, the maintainer of Make implied that the Guile integration was put there essentially as a hedge. People would ask for extensions to Make that he didn't want to commit to, so now the Guile is there so that people can extend make their own way.
I would imaging that the Guile stuff would be valuable to do complicated pattern substitutions than Make can easily handle. It is trivial in GNU Make to convert a variable containing a list of *.c files to a list of *.o files, etc. But something more complicated of that nature is where a Guile extension would come in.