The license that covers PAR is the Artistic License, and the way that it is used in this case fits the 8'th article of the Artistic License. Therefore it does not restrict your commercial use. Period.

However, as the final sentence notes, this guarantee does not necessarily apply to third party modules. If all third party modules are also available under the Artistic License (things that say that they are licensed on the same terms as Perl are), then you're automatically clear. Otherwise you might not be. Or you might be. It is wrong to assume either way. And that is what your IP lawyer's response does.

Whether third party modules actually cause you a problem depends on what their licenses say. And that will vary. For instance with a BSD licensed module you will be fine. If it is only available under the GPL, then you likely have a problem. Read the license and respect it.

In your specific case the question is whether the terms under which you have access to the proprietary module let you do what you want to do. I don't know that - it entirely depends on your agreement with them. Furthermore the choice of packaging application does not affect that - the copyright issue is between you and the people who own that proprietary module, the packaging application doesn't enter into it.

Therefore, as I think your lawyer will verify, there was no legal reason for you to have chosen not to use PAR. That was a misunderstanding.