Is it actually necessary to show that checkbox at all? Most if not all wikis set the property via templates, so normal pages actually never should use the __DISAMBIG__ magic word, and thus the checkbox never should be needed.

Just to add a few numbers: In de.wikipedia 3 articles had the __DISAMBIG__ keyword, all of these were added via VE, and all of these were wrong.

Perhaps we need to add flags like TOC , DISAMBIG and other behaviour switches into the metadata of the template usage as annotated by Parsoid, in order to at least be able to detect that these are already being added by a specific template call ?

That still won't help you find an appropriate template to for adding the behaviour, but at least will avoid you from adding it when not needed ?