Answer:
Yes, you can exclude folders and files from being checked by AutoRestore and quarantined using the Form at the top of the Quarantine page. See this video tutorial for how to do that > https://forum.ait-pro.com/video-tutorials/#autorestore-quarantine
It only takes about 5 seconds to exclude a file.
You can import/export BPS Pro option settings using the BPS Pro Setup menu > Setup Wizard > Setup Wizard Export|Import tab page.
AutoRestore|Quarantine exclude rules are not exported because the file paths are going to be different for each website. The BPS code is universal/global, but the DB entries (file paths) are not because that would simply not work correctly.
Example:
Website 1: /xxxxx/xxxx/public_html/website1/some-path/
Website 2: /xxxxx/xxxx/public_html/website2/a-different-path/