For batch scanning, I'd say something like a barcode has the advantage of being easier to detect for document separation. Our "cover sheets" actually have a barcode an a QR code mixed in with all the human-readable stuff so they serve a dual purpose.

A cover sheet can work perfectly fine, but depending on how everything is configured misprints/misreads could cause it to miss a cover sheet and not separate the documents. A poorly printed barcode can also be misread in some cases, but even when it is misread it is still detected causing the separation.