Yes, I would put the whatever.pl file in the bin directory, and almost precisely for the reason you give against it :-). This makes it possible for me to use whatever.pl directly in a script or system if I want that particular implementation. If you want to place a wrapper around it or reimplement it as "whatever", then that's fine, go ahead and I'll still be using the specific implementation I wrote my script against (and of course, if you're the admin there's nothing stopping you from linking whatever.pl to whatever, thereby forcing me to use the new implementation). Normal users will use whatever anyway and thus benefit from implementation changes directly.

Yes this can be abused, but it provides maximum flexibility. Polite requests over shotguns and all that.