Then game isn't great at racial allegories, yeah. The game is at its best when it tries to be a straight up sci-fi story with Connor and has a machine slowly question concepts up until its learning mechanisms conflict with its programming. It's a great, emotional story, and I got really attached to both Connor and Hank.
Markus' story doesn't work for me for a lot of reasons, but the biggest one is just that...robots aren't a 1-to-1 to racism. Like, at all. Maybe the story could've worked really hard to try to draw a parallel or two, but the story lives and dies on this comparison and it really doesn't do nearly enough to justify it.