True but contractually the right to sell or transfer those shares belongs to you, and they are legally required to be held separate from the shares the brokerage owns for itself. Even if the brokerage firm goes bankrupt, you can still transfer your shares elsewhere. The only way you lose out is if both 1) the company broke the accounting rules and the shares are missing, and 2) the amount missing is more than $500,000 worth of stocks. So basically, if the person you trusted to hold on to your money decides to rob you, you could lose your money. Same as a bank run.
Having read your linked article I figure you might consider this a stupid question, but: in the event of a total financial and/or societal collapse, what makes you think anyone will be willing to trade for anything as useless as precious metals? Stocks and bonds are backed by the ability of people and equipment to produce useful goods and perform useful services. Gold just looks shiny. The former are easier to delete, ignore, or forget about, but the latter isn’t any inherently more valuable.