As a white male engineer, I will tell you thing the that most white dudes like me fail to understand about micro-agressions- and the document was chock full of them-is that they are not really significant when they only happen once, in isolation, it is the constant, droning repetition of them that makes them harmful.
Asking someone where they're from isn't offensive when considered in isolation. But if 90% of the white people you meet ask you this immediately, while it comes up only occasionally or late in the conversation when meeting other people, it makes you wonder.
One thing my mixed race friends get asked a lot by white people is "what are you?". At first I found that hard to believe, but I've seen it happen over and over again--random chitchat at the park with a nice lady who stopped to pet my dog; for some reason she has to ask my friend "what are you?" She's too nice to say "not racist, how about you?" or anything harsh in response, but it makes my blood boil.
Imagine being expected to defend and define your presence everywhere you go.
So, yeah, the idea was harmless. The presentation was part of the constant barrage of gatekeeping behavior that women and people of color are sick of dealing with. That's why it's offensive, that's why people are angry.