> I'm often surprised by their height

Because they're of an unusual height, I assume. You had an expectation that they were of average height.

You can look at the pictures of the person that received that comment. They don't have an unusual skin color, and the ethnicity matches their name (say, they don't have a Russian sounding name with really dark, almost black skin). It shouldn't be unexpected to see their skin color.

Another option is that the expectation didn't come from averages nor names, and it came from prejudice about how software engineers look like. So yes, it definitely can be interpreted as a racist remark.