You make a lot of good points with regard to how DuBois treats race relations in The Comet. I agree that there is a definite segregation in both the beginning and the end of the story. Not just between the Jim and Julia, but between Jim and the world around him.
The bank president, in particular, is shown to be "above" Jim in how he "smiled patronizingly" at Jim in the very beginning of the story. The fact that a bank president would treat anyone not of similar social stature this way isn't the point, though. The point is that Jim feels alone in the world, that he is "Nothing!"
The middle of the story goes a long way to keep him apart, even as the two primary characters work together to get through the horrible time they are forced to endure together. At one point, Jill realizes she's alone with a stranger, and worse, "with a man alien in blood and culture." DuBois doesn't really want us to get too comfortable with the idea of blacks and whites interacting too closely.
The one moment that the two have that feels comfortable is at the end of the tale, when they're looking at each other on top of the Metropolitan Tower. She's has just had the epiphany that they will be the mother and father of the new human race. He feels like a risen Pharaoh, a god among men. She sees herself as this man's mate, and he sees himself holding a scepter.
While I feel like this particular scene is forced and completely melodramatic in so many ways, it was an effort by the author to set things not equal, but to put the black man in a position of dominance.
He then brings Jim's dream crashing down around him with the honking of a car horn and the bursting of a rocket. Suddenly, Julia's father and fiancé are there and we're back to reality. Jim is just a black man who is too close to a white woman for some whites' comfort. The division of the people showing up on the roof feels more to me like hope, than it does anything else. Hope for a future where a black man could be alone with a white woman without calls for a lynching.
And then Jim sees the black woman with the dead baby, and is overjoyed that she's alive. I think this final ending to the story sets everything back "the way it should be" with regards to race. This ending would have made the story more agreeable to a white audience in 1920. Their suspension of disbelief to enjoy the Science Fiction story is brought abruptly back to reality with Jim's "sob of joy."