Does time machine make a backup of files which are stored in iCloud, but not stored on your local hard disk (i.e. files which have been removed from your local hard disk when the 'optimise mac storage' feature is enabled)?
If you change a file it should show up on your local drive long enough for a backup. (Edit) I checked a file marked as only on iCloud and it is indeed on my Time Machine backup (Edit #2) An odd test scenario: I actually forced the file off of my local system "brctl evict testdocument.pages" Then I changed the file using iCloud.com. Within minutes it appears that iCloud on my Mac detected that the file changed and actually re-downloaded the physical file to my local drive. The next Time Machine backup did in fact place the iCloud changed file into the Backups.backupdb folder. I verified the file contents by actually examining the Time Machine file for change I made on iCloud.com.