No, you are correct. Other applications like the ones that I listed in my original post can add comments directly into the PDF that are viewable in Adobe Reader. In fact, annotation is part of the PDF standard. It is just getting Adobe Reader to activate its commenting features that is the problem.
That said, almost everyone has Adobe Reader or has heard of it. It is the same problem as trying to get people to use something other than Word; they will not want to install some other piece of software because they have never heard of it, even if that software is demonstrably superior. This is particularly bad in the Humanities where technophobia is rampant. So, getting Adobe Reader to unlock its commenting features would be a huge win.
As for moving publishers away from PDF, you don't. You bypass them by having your departments produce their materials without them. At least, that is my thought on the subject. Have your departments collaborate with colleagues in LaTeX then make that available in PDF on a website somewhere. The beginnings of that are already happening on Arxiv.org where most research is published in the sciences these days.