I don't understand two points you make in this article.

1. As you put it: Given an assumption that racism is primarily institutional and that efforts to end racism need to be made on an institutional level, how can we explain individual acts of prejudice—like job discrimination by a specific manager against a specific candidate for a specific job? I am looking at your question here, and I don't see why these two sides of the equation should be difficult to reconcile. We live in racist societies, so individuals who operate with racist assumptions have learned a lot of them from their society. A hiring manager may perpetuate the existing structural racism in their current or former workplaces. Consciously or unconsciously, the hiring manager prefers candidates who look like the people they've already worked with (or have seen on television, etc.). That person's individual racism isn't necessarily coming from some pure inner space in their head. If we gaze over their shoulder, right there, in the background, we see a racist society. So we cannot so quickly conclude that prejudice felt or expressed by an individual isn't also structural in origin (i.e. how the person became racist) and in effects (i.e. how they are feeding that racism back into social structures).

Of course, the human brain inevitably applies categories and labels, some of which become racialized, and these thinking patterns emerge in early childhood and are hard to break; this is discussed by Jennifer Eberhardt in Biased. But our personal neuropsychology doesn't cleanly separate from our social environment, so I think it would be very difficult to run a psychological test to separate individual racism from structural racism. Results that appear to reveal "only" individual psychology may actually be caused by something else.

2. When you move on to Anne Applebaum's discussion, specifically where she says that theories that emphasize structural racism "will not be able to explain why the U.S. did in fact have an Emancipation Proclamation," I think her question is properly applied to life in a much broader way. Generally, our theories have trouble explaining how any moral progress is possible of any type in any circumstance. It's a sort of Zeno's motion paradox: how can we go the distance if we haven't yet gone half the distance if we haven't yet gone half that distance... It's a question of inertia: how any of us, sitting with what we've been given, ever changes anything at all. Even if racism is mainly individual, we will still have the question of how racists can individually morally progress as well as how society can morally progress with them or despite them. And, yes, if racism is mainly structural, as Applebaum pointed out, we do have the question of how our institutions will ever change, especially if people's individual moral psychologies (their ethical beliefs, intentions, etc.) are assumed irrelevant to the question of how the group functions, because how is an institution ever going to change on its own, without the efforts of the individuals who make up that society?

The question of How does anyone ever change anything about themselves or their society? feels, to me, unnecessarily abstract, especially if you mainly want to talk about something more specific (namely, whether racism is structural). The question of moral progress can remain an open question about human life in general. "A body at rest will remain at rest unless it is acted upon by a force," per Newton's law, so it's hard to explain how anyone ever gets out of bed in the morning, much less how they get out of bed more ethically than they did yesterday. But my inability to explain this doesn't lead me to conclude anything about specific evils and immoralities. I can't, for example, conclude that racism is primarily individual rather than structural just because I can't explain how any person or institution ever changes.