I moved to Germany and learned that the "Where are you from" question is not a good icebreaker. As an immigrant working in an industry with lots of other immigrants, I thought it's okay to ask, but once you ask a German person of foreign descent this question they might perceive it as if I said they are not really German (sometimes context can make it even worse).

That's just propaganda by grievance activists, though. "Where are you from" is standard German small talk. Notice how effectively this method destroys communities, nobody dares to talk to each other anymore, for fear of saying something wrong.

I don't think it's just propaganda, I honestly felt a couple of times that I inadvertently made people feel bad. It's not like they threw a fit and called me racist (like the "grievance activist" implies).

Also, I don't want to say that anytime I asked this question I offended someone, it's more like 3% of the time I had this feeling that I wish I didn't ask.

Grievance activists teach them that they should feel bad, and it is communicated on many channels. But grievance activists should not dictate to us how to behave or feel.

Why would they feel bad or offended about you asking them where they're from? That's already a weird state for people's psyche to be in. That negative link between "asking where they're from" and the person having negative feelings is precisely the effect that the "propaganda" as OP called it is having on people.

Why are you supposed to learn about their culture, and not they about your culture?

Historically before the industrialization, being fair skinned was a proxy for being wealthy enough that you did not need to be in the field and work hard for a living.

After the industrialization, having a tan was a proxy for wealth. It showed that the person could afford being outside rather than working hard inside a factory all day.

Wealth and status gained from wealth is something which people inherently find interesting, and especially when there are changes. From a behavioral perspective, anytime people comment about someone tan I see it as a comment about status, similar to what happen if someone buys an expensive jewelry or car.

If they think darker==bad, they are the racist that should be reported