Symptoms
"Access Denied" on Appify with specific users.
A site owner, part of the AD SharePoint Owner's group set as one of the Site Collection Owner's groups is not allowed to appify a list. This seems like a similar error where the AD groups are not expanded by Appit to include those users, and therefore users have to be manually added to each site.
Diagnoses
AD/AAD groups were not properly synced.
Resolution
Manual run of "DirectorySyncClientCmd initial" for a fuller AD import.