There is a subtle point here that I think you are missing about license restrictions and the enforcement thereof.
Is it okay for a tool to attempt to enforce usage restrictions? There's no algorithmic way to determine if a particular intended usage is protected under the fair use doctrine or not. The flags on the content can't take fair use into account at all. If strictly enforced they are guaranteed to restrict reasonable fair use.
I can't recall any serious discussion among FLOSS licensing supporters about toolizing enforcement of the licensing terms in such a way that it would also restrict fair use of the code or executable carrying the FLOSS license. You have to remember that FLOSS licensing only grants you rights that you do not have by default under copyright law without a license.
It's not strictly the wishes of the original author that is the question. The question is the wishes of the original author insofar as those wishes are not more restrictive than legal doctrine allows. Content usage flags can't accurately encode fair use and any such flagging will be overly restrictive. There's no a flag can no if I'm cutting and pasting a section for scholarly research and thus protected by fair use.
But that isn't to say that the flags should be silently ignored. I think there's real value in making people explicitly aware when there is a use restriction in place, so they can decide for themselves whether their use warrants fair use or criminal activity. The biggest problem with our content consumption culture is that we haven't made any allowances for content licensing in the interfaces we are using to select and use digital content. It all gets lumped together and users of the content have no way to make informed choices based on licensing restrictions. Being able to present the flagged use restrictions as advisory information in the pdf user interface would be more inline with a model of informed decision making.