If they don't read, then they wouldn't be using Firefox, since all web pages (barring a few exceptions) would be gibberish to them :)
> And showing message box every damn time one site has Javascript/SSL
That's not what I'm advocating in that particular recommendation. I'm more advocating for some sort of heuristic analysis when Javascript is disabled. There are lots of sites that do silly things like rely entirely on Javascript for rendering text (for example); those should be easy-to-detect as scenarios where a warning would appear.
Also, most similar warnings presented by Firefox already (usually about outdated plugins and such) have a way to permanently dismiss, or to remember a setting for a particular website, or some other way to mitigate the understandable annoyance of always throwing warnings. A "don't ask me again" would immediately resolve the problem you identified.
> I think it's fine to have these options as extensions or even inside about:config, where the user would never disable by accident.
I think that's fine, too. My comment was more about identifying the correct cause of various effects - i.e. that the harmfulness of the checkboxes being criticized is due to their non-obviousness rather than their existence.