I know you mentioned that you don't support brackets in links, so this is a long shot... But I have hundreds of thousands of links in brackets! And I would very much like them to work with auto tooltip, how they were working previously... Maybe that was with the separate AutoTooltip plugin, but none the less...
Example of my links: [[books:bg:4:34|[Bg. 4.34]]]. Any other way to make it work than changing all of them?