In configure, you can override any tool location by setting the variable name on the command line (e.g. configure MAKE=/path/to/make). Configure also includes validation that any such argument actually corresponds to a valid variable and will print a warning if no match is found.

This validation logic is currently evaluated before the CUSTOM_LATE_HOOK is called so any variable defined there will still trigger the warning if specified on the command line. The validation should be moved to after CUSTOM_LATE_HOOK.