When we make the ADRs, we note the allergies that are available (such as gluten) and always click "other". When we arrive at each restaurant, the chef comes out and speaks with my wife, and they discuss options. We even bring a pre-printed card that lists all my wife's allergies (which ensures they get the full list).
In a few cases, if a chef doesn't want to make an effort, they'll just suggest a few items on the menu that they can pull together to make a meal. In most cases, the chef prepares something unique and special, which is great, since my wife can't dine out safely at home.
That's one of the things we love about Disney - the special care they have for people with food allergies.