The problem is they're simply not as conscious of the ingredients there as they are here. Food allergies and special diets are practically an alien concept.
Even worse, they might look at your card and, in the desire to please you, tell you the food is safe -- and they might mean it, too, because they won't recognize the specific ingredients on the list as being in the food. But they may not realize that those ingredients are in the ingredients, if you get what I mean.
I've had friends with special dietary needs who've been through all that in Japan. Maybe it's gotten better in recent years, but I wouldn't count on it.
And hopefully, someone else here can give you more specific information.
Good luck. I hope it works out for you.