In my experience, I've been able to swap out sides for other sides as long as they are snack credit eligible. I read the original question differently though. I thought OP was asking if they could order a snack-eligible item such as fries and add chili/ cheese if it would still be covered under the snack credit or if you would have to pay an upcharge for the chili/ cheese like you would if you were buying those fries OOP.
OP, since you specifically mentioned Casey's, the chili cheese fries are specifically listed on the menu as snack credit eligible, so there would be no upcharge. Chili cheese fries are also available at Restaurantosaurus in AK for a snack credit. Pretty much all single serving side items are considered a snack credit, so if chili cheese fries are listed on a menu, they will most likely be snack credit eligible, and also, at least in my experience, able to be swapped with the sides included in a meal. If what you are asking for is not specifically advertised on the menu or actually adds on to a menu item, like a cup of cheese dip to go with your snack credit bag of doritos, or adding bacon to your burger, the answer is YMMV. Protocol would most likely be that you are either charged extra by cash or by using an additional snack credit (for instance cheese dip can be purchased by itself with a snack credit, though it's obviously not a great choice from a value stand point); however, depending on the cast member, they may just throw it in as pixie dust. Personally, I've been pixie dusted the cheese dip years ago with a snack credit pretzel purchase (back before it was standard to include the cheese with the pretzel for one credit), and have never been charged extra for adding cheese to veggie burgers that didn't include it. My DD asked for cheese for her fries with her meal at a few QS places a few months ago (paid with QS credits). A couple places included it for no charge, a couple said they didn't have cheese dip (she didn't want shredded cheese- she's weird), and if I recall, only one place charged me, though they did tell me it would be extra before ringing it up. I was fully prepared to pay at all places, and I think it was only like $1 for the cheese dip the one time I was charged.
Wetzels pretzel stand in DS did charge extra for the cheese. Both pretzels and cheese are available as snack credits, but you'd have to use 2 credits to get both. I chose to get a pretzel with a credit and pay for the cheese OOP there.