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.
My color of skin definitely depends on the camera I sit in front of. The best cameras are as good as a mirror, but lower quality cameras built in laptops are awful. Looking at greenish or greyish myself is a bit nauseating.
I don't see the difference between that and realising someone is a different ethnicity than you expected.
Racism is (by definition) prejudice, discrimination, or antagonism. Being surprised because someone looks different than you imagined is nothing like that.