Yes, well if you read #1539 that was exactly the problem. The option "Ensure newline at file end" prevents empty files.
So we need to decide what's more important: - do we need to ensure a newline for an otherwise empty file - do we need to be able to create really empty files (0 byte size)
Both things are IMHO not very important. Let's make up a decision. If this is not merged then maybe also #1539 should be closed as "wontfix".