Could Parsoid help us here? Parser.php's replaceInternalLinks2() calls wfIsBadImage() as part of a lot of special-case link handling.

Can you help me understand why those images are not simply deleted? Is the issue that they are stored in Commons and wanted in some wikis but unwanted in others?

(In reply to Gabriel Wicke from comment #2)

Can you help me understand why those images are not simply deleted? Is the
issue that they are stored in Commons and wanted in some wikis but unwanted
in others?

The bad_image_list provides a built-in exception mechanism. See the second line in the file, and the "except on [article]" text that follows it: https://en.wikipedia.org/wiki/MediaWiki:Bad_image_list

The files without exceptions listed there, ie. not used anywhere on Enwiki, are indeed potentially used on other projects. Most or all of those files are stored on Commons.

Change 118565 had a related patch set uploaded by Matthias Mullie:
(bug 61772) MediaWiki:Bad image list not integrated

https://gerrit.wikimedia.org/r/118565

Change 118565 merged by jenkins-bot:
(bug 61772) MediaWiki:Bad image list not integrated

https://gerrit.wikimedia.org/r/118565