I think the server either didn't care/was lazy, or purposely let you order in a way that would be more expensive, thus padding her tip in a roundabout way.

i don't blame you for being frustrated. A good server will point out "If you order it X way, you'll pay the same price but you get a little more food," or other similar manners. I did it when I worked fast food, "I'm going to upgrade you to a large fries, because that combo is cheaper than what you just ordered."