You usually do tip on the full amount right?
Many cafes sell also beans and other merchandise that are manufactured or made in batches, and can be $20 per item. So tipping on those items would be similar than you tipping in grocery stores or other stores that sell goods. Like you buy a $20k car, do you tip them 20%?
Personally, I always just change the default calculation and tip on the service items like $1 for coffee/drink.
That said, it's sort of an arbitrary custom. It's not very much work to fill a glass of beer, find a t-shirt in some cabinet, or hand someone a cup of coffee.