At table service restaurants the menus will list the entree and everything in the description that accompanies the entree. Usually you can substitute one side for another if it is listed as a side on another entree. Further down on most menus is a list of sides/accompaniments with separate price points. These are items that you would have to pay for OOP if you order them.
As far as subbing an extra side for an appetizer, it would depend on the restaurant so you'll have to ask. You will probably have a better chance of succeeding at a Disney owned restaurant. The third party venues are less likely to allow it because they're reimbursed by Disney according to the plan guidelines and would not be able to submit an accompaniment as an appetizer.
