It seems like it would throw off recipe since you can fit more in once they are chopped?
The writer is unlikely to have thought about it. They'll just write down what they did as they did it, in what they (sometimes erroneously) think is clear language. If it bothers you - and it's unlikely to really matter unless the ingredient is essential to the chemistry involved in the recipe - then consider how they're likely to have made the recipe themselves. It would be silly to chop some unknown quantity of nuts then measure a cup of them. You'd start with a known quantity, then chop them. That is, unless you buy a packet of them ready-chopped. So I suppose the answer is, use your noggin.