But why should you even be able to set a persistent preference, that will apply to every subsequently loaded file, just by clicking on a button in the main UI. (Note that the preferences are stored in about:config in Firefox, hence they will apply to all loaded files.)
Just because I click on a button to use a particular function when viewing a PDF file, that doesn't necessarily mean that I would want that specific function to be applied to all other files. Doing this would also, most likerly, be confusing to many users.

To be able to set preferences, I've always intended to submit a follow-up PR that adds a UI for viewing and setting preferences from within the viewer. (I've previously created a mock-up, but wanted to see whether this PR would get accepted before spending a lot of time on it.)

To summarize: I never really intended that the preferences should be set straight from the viewer, since I believe that would be confusing to many users.