This might just be an issue of regional vocabulary though I'm sure it's used in the presumptuous way you describe as well, the underlying question isn't necessarily unfriendly or borne of a discriminatory attitude - in a Midwestern town right now, but I can recall a few weeks ago actually this exact conversation between my American friend who's from a Pakistani background and a female census taker who was from South Asia.

In her case, she used the exact same vocabulary but it was much more obvious she didn't mean to imply that they weren't native born because she herself was not native. Context is important in conversation, but there is such a thing as regional mannerisms. On the west coast my vocabulary was certainly brought up for being just a tinge different.