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Adobe does not condone any illegal circumvention of document encryption or copyright.
If an author decides to secure a document, of any format, to prevent users from altering it; Adobe software respects that decision. Commenting is alteration, as not only are you adding items to the page, but you can use comments to obfuscate the original content (for example by covering text with a new text box). It is not technically possible to restrict only certain types of annotation, or to detect the result of an annotation on a page as interpreted by a reader.
If an author exerts his or her right to prevent alterations to a copyrighted work by applying technological measures to a document, bypassing that protection is a criminal act in many countries (for example in the USA, it is covered by DMCA).
With Adobe Acrobat, and now with Adobe Reader X, the default position is to allow comments on any unsecured PDF file. In the past, files without specific Reader-extended permissions could not be annotated in Adobe Reader, but this was requested by users and implemented with the Acrobat X Family. Encrypted documents are therefore assumed to be intentionally thus, and Adobe software enforces that policy without exception.
Thank you for your detailed answer!
Based on what you explained, I'll have to go to next step, i.e. post a request to allow simple highlighting and commenting in any PDF document.
My question now is, where can I post my feature request to allow highlighting and commenting in ALL PDF documents?
A suggestion would be to only allow highlighting with transparency to avoid hiding of content. I am convinced that it is also possible to find a technical solution for this productivity tool.
Let's be honest, depending on what's at stake, there will always be a way to falsify a digital PDF document. I'm not in this business, I only want to stress the practical aspect of this matter.
Why lower general usability and productivity for this percentage (30%? 40%?) of strictly confidential and not-to-be-altered documents?
If one really want the content to be secure, one will sign it with a certificate or some other kind of hash, but why deactivate daily productivity tools of the software?
It's never going to happen. If a PDF has a protection flag restricting changes, Adobe software won't make changes. Period.