I too find the empty folder creating frustrating. Even more frustrating is that SyncToy 2.1 (and prior versions) are too stubborn and will not let me uncheck the boxes on folders. I feel that SyncToy should prioritize folder creation first; if
I make a mistake and uncheck a folder from the "New" list but still have a file that should go into the folder, then SyncToy should make a default decision. Document Microsoft's call - either create the folder and copy the file *OR* ignore the file copy
error and essentially don't copy the file. Since SyncToy is not a robust copying solution (as it allows human intervention), then it is my responsibility, over multiple syncs, to figure out what I have and what I need.
On the other hand, most backup programs I am aware of are smart enough to figure it out - they grey the folder action box if a file in the folder is selected. I'm sure that the programmer(s) who drafted SyncToy could do that too, even if it is an unsupported
PowerToy. If you can, see Iron Mountain's online backup; Connected's online backup, and I think Acronis local backup have the behavior I seek.