How do you sync form DT3 to iCloud maintaining the same folder structure?

This seems like a helpful thread: Backup Strategies

@chrillek could you clarify how you ensure that Time Machine only backs up changed files?

I know that Time Machine is particularly efficient with APFS cloning - see Why nothing else can back up to APFS like Time Machine does – The Eclectic Light Company. Which leads me to believe that backing up without carefully considering how to export the files could cause Time Machine to back up every file, not just the changes. For example, I could create my backups by simply selecting the entire contents of my database in DEVONthink and dragging it onto my desktop, and then perform a Time Machine backup. Then before my next backup, I could do the same thing, replacing all those files with new ones. Does Time Machine know that some of these new files could be identical to the old ones?