With the privacy settings, yeah that’s true, though it would be pretty out of band for someone to accidentally exclude the ordinarily invisible ~/Library/Containers/com.literatureandlatte.scrivener3/Data/Library/Application Support/Scrivener, or some partial range of that! 
Well, a long shot is a slow trawl of the Time Machine drive itself (since I think Apple still has not created a way to search through directly). I describe doing so in this post. The find command described there would be necessarily different since one is looking for Formats instead of projects, but the rest is all the same:
find /Volumes/TimeMachineDrive -name "*.scrformat" > ~/Desktop/potential_support_folder_locations.txt
As for what “TimeMachineDrive” should be, obviously that should be substituted for whatever name the drive goes by when typing in ls /Volumes as a command.
The same time caution applies, and in fact I would consider not searching the whole drive, but only the latest dated snapshot by adding that part to the path after “TimeMachineDrive/”. What would take many hours searching your whole Mac could easily take many times over that, when searching through a sea of copies upon copies of it. But it’s the sort of thing you can leave running in the background for days without harm or slowdown.