Can I embed PDF files stored on AWS S3 without their URL being public?

Yes, this is possible under the following conditions:

• The bucket in AWS S3 must be publicly accessible.
• The proxy must be activated in the plugin settings under File types > PDF.

As soon as this is fulfilled, every file hosted on an AWS S3 would be recognized as an external file and delivered via the proxy. The URL behind the proxy is not publicly recognizable.