A customer's checkout failed because a dish sold out while it sat in their cart. Can I say sorry automatically?

Yes, with the sold out apology. When a checkout fails for that reason, a customer who has ordered before can be sent a small single use code with an explanation. Each customer can hold one live apology code at a time, and the codes are ordinary coupons named SORRY followed by six characters, valid for seven days, visible under Marketing → Coupons like any other. Switch it on under Marketing → Loyalty & stamps. The Loyalty & rewards tab in the docs explains the sold out apology.