My experience with other languages is that machine generated flow charts are seldom useful for anything but satisfying a customer requirement for a flow chart. They must be isomorphic with the code. This is not at all the same as a hand drawn chart, where its designer comunicates his understanding of the code (often by intentionally omiting details.)
I believe that formatting your code with the CPAN utility perltidy would be more useful than rearranging the code into a flow chart. Clearly, this is a matter of opinion which you must decide for yourself.