This is the domain of DRM/whitebox cryptography, and leaving aside all discussions about the feasibility of such efforts, PDF's implementation of it can safely be assumed to be broken – the master key used can be found in several open source PDF tools' source code and on Stack Overflow, among other places.

I assume the attacks presented in the paper are about the other type of PDF encryption, which requires a password to even display the protected content, which could definitely be done in a way not vulnerable to the attacks described.

https://www.pdflib.com/pdf-knowledge-base/pdf-password-secur...