If the genersted PDFs are stored encrypted in an accessible server with proper access control, then that is a measurable improvement over email containing medical informstion that a random citizen would send, which would be bouncing around unencrypted around at least one third party SMTP server. Of course, if then that person uses an online Fax service, they are sharing that information with at least one other party...

And that's even without considering the security benefit of not receiving files that could be compromised, instead generating a file from an image stream. (Now I'm trying to picture what a daisy chain of exploits would be needed to craft a malicious Fax.)