I think it would be best to simply change the wording of the first paragraph of the page. Clearly, if the style guidelines state that the full opening tags should be used, the short tags should not be "recommended" for any purpose (and really, what are you saving here?).
It seems clear enough to me that the note on the possibility of short tags being disabled is intended as a troubleshooting note if they don't work in your environment. Maybe some additional information could be supplied to let people know which versions support that option, but in context it doesn't seem to me that the information is necessary (just nice to know if you're worried about such things).
I think the major confusion here comes simply from the fact that the page was created to document a feature of CodeIgniter (the capability to expand short tags in views) which is obsolete in current versions of PHP, but which may still be relevant for some subset of users.
