I reached out to Omnigroup and here is their response:
Thanks for getting in touch! You’re both exactly right—there was a setting that was exposed in OmniFocus 1 for processing completed Inbox items into a SAL-type project called Miscellaneous.
You can enable this (synced) setting via the following URL on any platform:
Note that OmniFocus refers internally to the “Miscellaneous” project by its unique ID, so you can rename and move it if that suits you and the completed Inbox items will end up there.
I hope that helps! If you have any trouble with these steps or have further questions or concerns, please don’t hesitate to contact me. We really appreciate your support!
The Omni Group
I ran the url and let omnifocus create the Miscellaneous SAL. After that, everything seems to work. I ran it on my iPad also.