Trying to keep track of where Apple puts things is confusing (partly because, on the drive you boot from, it apparently won't "find" files in the Mobile Documents folder). So I'm doing a little experiment.
First I searched for a file that is in one of those Apple create application documents folders in iCloud. Searching with the finder, it found the file in two places:
In my backup of my internal drive in the Mobile Documents folder. Since it is an exact copy of my boot drive, it must also be in that folder on the boot drive - but Finder won't show it.
Next I searched for a document directly under iCloud (not in another folder). Same results.
Then I searched for a file directly under icloud/documents. This gave a different result. It found one within iCloud, as expected, but the other one was NOT in "Mobile Documents". It was in my backup, but under my user folder/documents. It didn't show up in my internal drive, though it must have been there since it is in the backup. I'm assuming anything in a hidden folder on the drive you boot from just doesn't show up. Not even if you have unhidden the folder. This is what really makes things confusing to me. If I didn't have a backup drive it could search, I wouldn't be sure it was stored on the Mac!
Finally I searched for a file inside of a folder inside of iCloud/Documents. Same result as the previous example.
Summary: It seems that any file directly under "iCloud" will be backed up in the Mobile Documents folder (which you can't actually search) on the Mac. But anything stored under "iCloud/Documents" is searchable and will show up under "documents" on the Mac.
I'm not positive about one thing. While I assume to get that documents folder to sync, you must turn that on as I did the other day, I'm not positive the stuff synced to Mobile Documents does that without turning on that syncing. From what you write, I assume it does, but I don't really know for sure.
If so, then you can match everything in the cloud and on the Mac simply by not putting any docs in the documents folder. With these two options in mind, I'm really not sure where any advantages/disadvantages are to each approach. Other than doing it my way does at least let me see those files on my Mac.
Since you said your documents sync is off, can you confirm the files in icloud are also in the Mobile Documents folder? I assume you would have to have a backup to search to tell for sure.