Wikimedia Bugzilla is closed!

Sanitizer should have a (black)list of ids used on user interface (outside bodyContent, + TOC & categories related), so if it finds out same id inside bodyContent, it should trim it out. Or optionally return error/warning so user will be informed there's error in wikitext.

Also another way, how to enforce not using of MediaWiki built-in ids is to rename all of them to certain form, I'd say with some prefix, such as "mw-<current_id_name>" and then Sanitizer simply can trim out (or return error/warning on) every id beginning with this prefix. But this is huge compatibility issue and would need to be solved carefully, preferably with some promotion before - list with old -> new ids, so people could fix their scripts, stylesheets and tools.