From the article (ok the email):

Custody

If you buy a share of stock in a company, you don’t get your own tiny fractional share of all of the company’s assets delivered in a bag to your door. With rare exceptions, you don’t even get a paper stock certificate. Instead you get an entry in the computer of your broker reflecting that some of the shares that the broker holds are actually held for your account. But the broker doesn’t have a bag, or a paper certificate, either. The broker has an entry in the computer of some other intermediary—in the U.S., generally, the Depository Trust Company—saying that some of the shares that DTC holds are actually held for your broker’s account. DTC may have a paper certificate, though often it just has an entry in the computer of the company’s transfer agent reflecting that many of the company’s shares are owned by DTC.

I guess if any of these computers crashed then that would be bad? For you? Presumably they keep backups. This system actually works really well; there are occasional weird glitches in which the technical details of stock ownership can get confused, but there are not really cases of people losing their shares because their broker or DTC or the transfer agent forgot where it put them.

This is not an accident: Reliably keeping track of security ownership is a really really really important feature of the financial system, and so the financial industry works together to maintain a functioning system, and it is all heavily regulated to make sure that it works. This system is conventionally called “custody,” which is sort of a historical metaphor suggesting that you own paper stock certificates and your broker is keeping them safe in a box for you. But, in almost every case, that’s not actually happening; that’s just a metaphor. Really “custody”—the methods that your broker, and the financial system generally, use to keep your securities safe for you—occurs entirely on computers, and is basically an agreed and regulated set of legal and technological conventions for making sure that everyone knows who owns what stocks.

Cryptocurrency has different conventions. Basically there’s a blockchain recording who owns what, and an enormous set of possible numbered accounts each with, in effect, a password (a private key) entitling its owner to use the cryptocurrency in the account. There is (generally) no centralized intermediary holding everything for everybody; distributed technology and cryptography are what keep your coins safe. There is a lot to like about this—it is not vulnerable to single points of failure, it is not captured by powerful incumbents, etc.—and crypto enthusiasts quite vocally like it. There is also, to be fair, a lot to dislike. You can lose your password, or someone else, absurdly, can guess it. Maintaining your password yourself might be a pain so you might rely on someone else to keep custody of your coins, and they might lose them. In fact there is a comically long history of people losing their cryptocurrency because they or their broker or their exchange forgot where they put them. The actual experience really is much worse than in the securities industry.

So far. You could imagine better conventions for just, like, how your broker should write down the password or whatever. Getting to institutional-grade custody of cryptocurrency is not an unsolvable problem; it is just a matter of finding some good legal and technical conventions, and getting the industry, and the regulators, to buy into them. It is a hard problem mostly in that the industry, and the regulators, are used to the conventions that work for regular securities, and it is hard at this late date to get them all to agree on a new set of conventions for a new sort of asset.

Anyway here is a joint statement from the SEC and the Financial Industry Regulatory Authority on “Broker-Dealer Custody of Digital Asset Securities”:

In particular, a broker-dealer may face challenges in determining that it, or its third-party custodian, maintains custody of digital asset securities. If, for example, the broker-dealer holds a private key, it may be able to transfer such securities reflected on the blockchain or distributed ledger. However, the fact that a broker-dealer (or its third party custodian) maintains the private key may not be sufficient evidence by itself that the broker-dealer has exclusive control of the digital asset security (e.g., it may not be able to demonstrate that no other party has a copy of the private key and could transfer the digital asset security without the broker-dealer’s consent). In addition, the fact that the broker-dealer (or custodian) holds the private key may not be sufficient to allow it to reverse or cancel mistaken or unauthorized transactions. These risks could cause securities customers to suffer losses, with corresponding liabilities for the broker-dealer, imperiling the firm, its customers, and other creditors.

These are not problems that are so different from the problems of keeping a list of securities at DTC; it’s just that those problems are familiar and the crypto ones are new.