The definitive answer is --maybe---
It will depend on which restaurant you are at. In general, the restaurants owned by Disney are more likely to accommodate these types of requests. For example, most of the resort hotel restaurants are owned by Disney, and they will allow smoothies and "virgin" blender drinks for the dining plan beverage. They might allow appetizer-as-entree.
But the non-Disney-owned restaurants are more likely to be sticklers for the exact components on the dining plan. It was explained to me by a manager that the way the contracts works, the restaurants must prove they served the correct components or they will not get reimbursed...and all the systems must agree with each other. So if your dining plan says you get an entree, a dessert and a beverage then the order/receipt must show exactly those items. So they will not sub an appetizer for an entree, because they cannot enter an appetizer as an entree, it's not on the entree list (same reason they won't sub anything for dessert) ...and they tend to stick with exact list of beverages allowed : coca cola soda fountain choices, plain tea and plain coffee. No specialty beverages, no fancy coffees or teas. That I think is more a matter of them trying to squeeze maximum profit out of the plan...they have agreed to provide the meal/drink and are giving exactly what the minimum they can with the beverages (the coke drinks, plain coffee, etc. are just pennies to serve...the fancier drinks cost quite a bit more in both ingredients & effort.)
The non-Disney restaurants would be many of the Epcot World Showcase restaurants, and most of Downtown Disney restaurants, as well as the restaurants at Coronado Springs. Yak & Yeti and RainForest Cafe at AK are also non-Disney owned restaurants.
Bottom line, it never hurts to ask...there's always the possibility of exceptions being made, just wouldn't expect it to happen at non-Disney restaurants.
