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.
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.
"Assume the worst" = This is precisely the kind of mind reading that leads to a paranoid, unhappy, eternally vigilant society.
Everything is blue if you wear blue tinted glasses
I live in a city where I expect everyone to be expectedly dark, and anyone that come near to my white shade is very unexpectedly light
If I go to the pale end of the country, any darker skin would be unexpected, no matter the job title and no matter the IQ level
No unexpecting person should be liable for your projected meaning on surprising turn of events
When you meet a software developer, saying they're unexpectedly dark strongly implies you didn't think someone of that ethnicity was capable of being a software developer.
It doesn't need to be spelled out -- the implication is very clear, and if an employee claims to be ignorant of this, they should at least be sent on the race awareness training.