There's no way around it: some people will opt to entrust their BTC to third parties for storage, and some of those custodians will employ fractional reserve.
Far too many people already entrust their BTC to third parties. Coinbase is rapidly approaching 1 million BTC of customers' funds which it is holding on their behalf, which is utterly ridiculous. As the link you shared pointed out, exchanges have already been caught lending out customers' funds without their knowledge or consent. I wouldn't be surprised
at all if Coinbase were doing this too, given their long history of shady activities and complete disregard for their customers. You can add that to the list of risks when storing your coins on an exchange or web wallet - if there was a sudden down turn in the markets, your exchange might just find themselves unable to recoup what they've lent out and therefore unable to process your withdrawals.
We already have fractional reserve operating in crypto. For example, Bitfinex and Tether are no longer peddling the lie that USDT is backed up 1-to-1 with USD. They openly admit that it is only fractionally backed up, and even then, including by a variety of non-USD assets. If everyone who held USDT tried to cash out, it would essentially trigger a bank run, the price would crash, and many would be left holding bags they couldn't sell.