To enforce a policy for perl source files on a make source file is not a good, umm, policy.

Use the right tool for the job. Emacs can set rules for indentation, syntax, etc based on the type of file. I believe that vi also allows you to do that. Do not run perltidy on your makefile, run maketidy (is there such a beast?). Same as you would not run htmltidy, lint, or other inappropriate code cleaners on your perl file.