I think you can obviously wear them OP, as so many have said. But, its not the intention of the dress code.
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For the Signature Dining Restaurants, a "Business Casual" dress code is in effect:
Men - Dress pants, jeans or dress shorts and a T-shirt or long sleeve shirt with collar is required. (Jackets optional.)
Women - Jeans, skirts or dress shorts and blouse, sweater or dress is required.
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Dress shorts, not the shorts 95 percent of the people wear there. While it says Ts, it says business casual, which definately leans to a collar. If you're wearing dress pants or jeans for business casual, and even dress shorts (think airline workers) you're not going to wear crocs or flip flops. Thats not appropriate. Not only will it look off, its not in the spirit of the dress code.
Disney isn't going to turn you away, its not what they do, but crocs are not the intention, I am positive of that. If they wanted you wearing something like that, they wouldn't even bother with a dress code. When I've been to signature dining I see most people wearing collared shirts and the like. If I saw someone wearing crocs, they'd look out of place, and I know most people don't care about fashion on vacation, but these specific restaurants are asking that you do for that dining experience. If thats beyond your ability or desire, its probably best you don't go there.
The rants regarding this opinion I have should consider its Disney asking you to behave this way. Its the same in many work places. Its not that its personally disturbing, its just the expectation is set, it is nice if you follow it. If you disagree with it, write to them and complain. Its just another one of those things though, you can either follow the rules or not. If you're going to break them, and I dont think anyone can possibly rationalize their shorts from old navy or AE and their flip flops or crocs are business casual, just break them. Don't ask for an opinion. Some people might notice and chuckle at your fashion faux pas, but I'm sure it wont ruin their vacation or meal, it wouldn't ruin mine. It just singles some out as either not knowing or unwilling to follow the suggestion of disney.
Again, I dont think anyone can possibly rationalize their shorts from old navy or AE and their flip flops or crocs are business casual.