In the past, we had a good experience with restaurantasaurus (sp?) in AK. I do think they've changed recently, as I didn't like our meal last year. But in the past, my DS couldn't eat the chicken nuggets, but wanted the kids' meal (he was under 10 then). The manager came over and spoke to me, substituted a hot dog (no bun, damn Disney uses Interstate bakery, which makes Wonder bread, which a few years ago added dairy to all their breads) for no extra charge. Plus, when she went back to the kitchen, she had them change their gloves to put together my son's meal (it was even written on our ticket "change gloves"). I really appreciated that.
My son does well with Japan's Yakitori House (although I think their food has gone downhill so bad that I don't like it), but he loves rice and their chicken is safe for him, the service has always SUCKED but that is fine, my DH is Korean and some Korean restaurants have great food but horrible service.
I don't think calling ahead helps for CS at all. And it's really hit or miss - I didn't know about Divvies as an alternative for desserts anywhere. Most places, last December, they said all we could get was a chocolate chip cookie (which my DS can't eat) so many went in the trash at the end of the trip. That is annoying - I would have loved something HE could eat! No one wants that nasty no sugar added applesauce - eeeewwwww.
We ordered Divvies cupcakes for a birthday party a year ago - I felt too lazy to bake for my DS. Well, the kids liked them well enough, but they were dry and tasteless if you ask me. I'd rather have baked my own; I make pretty good dairy and egg free cupcakes, and the Divvies are not cheap. Lesson learned.
There is a gluten/dairy/egg free cookie to DIE FOR from Alternative Baking Company in the US. I don't dare buy them, as I'd eat the whole thing - they are huge and about the calories of 2 poptarts, and they are moist and so good! I don't know if WDW carries them (doubt it) but I think
Amazon does.