I don't see the problem with trusting the exchange as custodian of my coins for 12/24 hours (if I wanted to), if I already trust it as the custodian for instant exchanges. They still have the coins, only the period of time they are in possession of them changes.
The main difference is in the amount of money they'll be holding for that time. The 24h volume now shows XMR 24212. If a transaction takes 10 minutes (let's take the average Bitcoin confirmation time for this), it means they hold on average XMR 168 (or the Bitcoin equivalent) of their customer's money. If you add a 12 hour waiting list, this amount very quickly goes up a lot.
If there are no reserves for the coin I want, the exchange has to send back my deposit. I then have to deposit a second or third time if I am unlucky. That's throwing away money on fees.
That's a good point.