During the 2016 Doing Digital History summer institute, a demonstration about the use of collaborative markup web tool Hypothes.is prompted questions about whether an author on the web could somehow disable comments made with this software. There was some discussion about why someone might want to protect content from being marked up (even if it isn’t visible to most users).
Assuming that someone wants to protect their content from being marked up by users of Hypothes.is, there is the only way I could find to serve content that is invisible to the program.
The trick is to wrap your content in an iFrame. Essentially, this embeds the content within a frame that Hypothes.is does not interpret as text that can be commented upon. I don’t know how this would be applied to different types of content, but I think it could be made to work.
Here is an example of an iFrame with HTML content embedded and not available for markup using Hypothes.is: