However, I'm unclear from the changelog and I haven't found any other documentation about how to restore the functionality that this option used to enable. I have tried
ido-completing-read-plus/ido-ubiquitous, but that is overkill because it tries to enable ido everywhere, but I just want to re-enable ido for org-mode completion (mainly refile). I also run into the same problem if I try to set the completing read function to the one from ido globally.