As a thought exercise, consider that I can borrow your stock and sell it right back to you short. We can repeat this process a million times. 1 million shares short now based on 1 share.
This is not naked shorting because borrowed the stock from you each time with you willingly participating.
Certificated stock is slightly less fungible than shares of book-entry stock; because I probably want you to return a single certificate with my shares, and you may have to separate or combine certificates which takes time and money. One of the many reasons certificated stock has been on the way out.
That is why the system needs something like a block chain semaphore.
Imagine a company with 1 share of stock floating. Abel buys that share and loans it to Baker (via Abel's broker). Baker borrows the share and sells it to Charlie. Charlie loans their share to Diane. Diane sells it to Earl. Earl loans their share to Fred. Fred sells it to Gary...