The common usage of Devel::Cover is to determine whether the tests cover all the code. So why not run your code from a set of tests, with each using different combinations of command line options? That way, you can run the tests again any time you make a major change.

It's one thing to say, 'we used the --verbose options, therefore line 67 was invoked'; how does the --verbose option modify data structures? Is there some side effect you can verify in test?

Rather than running the whole program, is it possible to treat it as a module, and just invoke one subroutine at a time? That makes testing a lot simpler.