If the customer had no intentions of putting crackers or anything in their soup, could they "request" that it be filled almost to the top of the container? And would they be charged more for that?
Not at Wendy's. They have set prices for things and don't have a way to charge for a "little more". My suggestion would be to buy a large chili and have them put it in the small cup.
Maybe Mom and Pop type place would be able to do that. Restaurants set up their prices based on food costs. If they are charging for one size and customers want things filled to the top then they are losing money on each "full container". That adds up if there are several a day each day of the year.
Even back when I managed the Wendy's I set up a page out of the manual that had the required weights for fries for each size so the customer could see it. I also had a scale next to the fry station so that each employee could weigh the fries and the customer could see they were not getting cheated. Most restaurants do not do this and the fries are usually overstuffed. I did find though that by letting the customer know what the "official" serving sizes were and that by being consistent, they were less likely to complain. I also had the best food cost control in our region back then because I expected my employees to follow the rules.