“Chief Justice Roberts raised the point that corporations can actually file racial discrimination claims. So he said if a corporation can have a race, why can’t it have a religious claim? The government’s attorney didn’t really have an answer for that,” Ruse said."
He had an answer - he just didn't say it. The answer is that corporations can have any privilege that best serves the needs of the State. So if it serves the needs of the State for corporations to have a "race" - then bingo, they have a race. And if the State decides someday corporations cannot have a race - then bingo, they can't. That's corporate law. It is EXACTLY the same as a person running a business, and deciding some division will sell cars one day, then sell soap the next, and then go back to cars later. Exactly the same.
So given this definition of terms, Roberts was basically asking the government lawyer if he could think of a reason that would benefit the State to extend religious privileges to corporations, similiar to the way race privileges were extended to corporations - and the government lawyer couldn't think of a reason.