I think Japanese people who compliment on chopstick use are genuinely impressed. They figure that, as a Japanese person, they have a lot more practice at using chopsticks than a foreigner (and rightly so) and are amazed that you have developed the ability to use them naturally. They would be similarly amazed to see a gaijin speak perfect Japanese. I think it's justifiably noteworthy when someone can do well at something that isn't native to them. Using chopsticks is a skill and it does need to be learned. I don't think anyone uses chopsticks well the first time they try.