Hey, Sam here, CTO of BitMEX - we're a crypto derivatives exchange that's been open since 2014. When we founded BitMEX, we went through a long period of discussion among the partners on this topic. We were just coming off the low of watching the MTGox heist and it it was obvious that wallets were becoming the #1 point of failure on any exchange.
Ikeboy(sibling comment)'s explanation is as good as you'll get, in my opinion. And you can even skip steps 2 and 3, as we have done for two years on BitMEX.
It's our opinion that customer funds are simply too important to expose to this kind of risk, so we process withdrawals only once a day from airgapped multisig wallets. It's a bear, and it's slow - we developed a few internal tools to make the review process easier and separate signal from noise - but aside from some manual work we've never had a problem.
The #1 surprise, to me, was that customers don't mind the inconvenience. Sure, a few wonder why they can't simply get their funds immediately. But it's explained to them, they seem to appreciate the sensibility of managing this risk seriously. Compared to alternatives like ACH, at least it only takes one day and runs on weekends.
I can't imagine a nightmare worse than losing millions of dollars of other people's money. I hope for Bitfinex's sake that they are able to recover a portion and continue operating. We've spoken personally with much of the team and enjoy the relationship. They - and their customers - don't deserve this loss.