Can I customize the PDF of my submissions?

E.g., can I add our company logo to the PDF, or format the look at all?

Yes you can customize PDF report. Inside of this guide you can find how to do it: 

How to Customize PDF Submissions Report

You can also show headers, text and images form your form inside of PDF report:

How to Show Headers and Text in the PDF

Hope this will help. Let us know if you need further assistance.