As written your first example is ambiguous, because it could be you were trying to indicate that the second and third arguments are anonymous array references.

My question would be: does anyone really use these BNF syntax diagrams? They seem to be provided at the top of unix man pages primarily for the purpose of confusing newbies.

What you really need to do is provide examples of the way you expect the code to be used, combined with a written description of each of the arguments, indicating whether they're optional and so on. Demoing the use of "undef" as a placeholder is a good idea: that idiom is not at all obvious to beginners.

(By the way, it's probably bad form to have more than three or so positional arguments. If at all possible, I would suggest redesigning to use "named options", i.e. an optional hash reference of options in the last place.)