Filtering in the Synchronize tool is file based. You'd need to ensure all the files have the label in question, not just the folders, if you wanted to use labels for this.
But why not just start the sync one level down? Or filter by path/location?
Also, if you're only synching in one direction and just want to copy everything new, the Copy UPDATEALL command will be quicker and easier than the sync tool. That will let you filter by folder label, unlike the sync tool. (Using the subfolder filter clause is best here, as discussed in How to filter items by location or sub-folder )