There's the small talk version of that, but then there's the following question of "where are you really from?" if you give them a less exotic answer than they were expecting.

Edit: wording

This has been exactly my experience. 'Where are you from, where were you raised?' are the first questions after 'where do you work, what do you do for a living?'

As you well know, it's more the how than the what.

If you are white, then take how many times you get asked "where are you from" and multiply it by 10. Then decide if you don't think it would get annoying.

It's rarely out of malice. But that doesn't really matter. If you get asked it enough, you will start to feel like you don't belong.

There aren't enough people here to do that (that I actually speak to at least).

As an aside, I have a last name with an unusual spelling. Literally everyone who sees it asks how it is pronounced, followed by where it is from. It is just a fact of life.

By asking the question, people clearly want to know more. Sure, they might be asking the wrong question, but the reality is, they are trying to include you.

If people didn't want you to belong, they would just make the assumption on their own and not ask (and probably avoid talking to you altogether).

Surely you've experienced personally or seen firsthand the following microagression on a regular basis living in the midwest as I have, in a city that reliably votes 85% democrat no less:

"Where are you from?"

"Cleveland Heights."

"No, but like, where are you from?"

implying that this brown individual must surely have wound up from some far flung corner of the world, and that they couldn't have possibly been a native born person.

I actually have been asked what country I am from. I don't have a heavy accent (there are far heavier than mine further out in the boonies) but apparently enough of one.

What of it? If you have some characteristic that is unusual (within a group such as local community) people will notice and be curious.

That is basic human nature, not lack of friendliness or malice.

It's prodding into personal details that many draw the line with. You might not have a problem with it, but I've personally heard from a few different people how they get annoyed with those sorts of questions being leveled at them all the time, simply because they didn't look white. Aziz Ansari even joked about this a few times during Parks and Recreation, it's such a common phenomenon. Imagine seeing someone who might have some sort of disability then asking them if they were insert disability you are unqualified to diagnose but assume they have. That would be considered pretty rude.

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.