How to exclude fields from print page version (html, pdf)? As in question, excluding node fields from HTML print page is easy via CSS, but what about PDF version (PDF version module)?
A quick peek in the code shows that the Print module utilizes "View Modes", which is a good thing. More info in Entity view mode and Drupal 7 custom node view modes.

You should create a new suitable view mode or re-use one you already have. This allows you to control the settings with the Field UI, while still allowing you custom templates if you need to.