If you take money out of your 401(k) to buy gold and silver - that withdrawal is a taxable event. You'd have to pay penalties on that transaction.
By rolling over funds from a 401(k) and into a self-directed IRA used to buy precious metals (a gold IRA), you can defer taxes. The money is moving from one tax-advantaged account and directly into another.
I suppose either way, eventually the IRS gets their hands on your money!
But I see some advantages to opening a precious metals IRA vs taking the cash out and using it to buy gold. All of my real savings outside of an emergency fund are tied up in the 401(k), so that's my only source of money to buy gold and diversify my investments.