I think you're missing the OPs point.
This is purely anecdotal, but I grew up in a military town. As a consequence, all of my peers and many of my friends were of mixed race, color, and creed. I don't recall segregating my friends based upon the color of their skin. I do, however, recall a strong bias against children that weren't in my same age group. I also vaguely recall flipping out when I was very young when I was taken to a store and saw a man who was blind in one eye (it was pure white). Children discriminate based on things that don't match up with their own experiences, and I was no exception. I certainly never treated my mixed race peers any differently; I grew up with them.
While the t-shirt experiment is interesting, it lends credence to my own experience. Children will categorize things and some things (age) are little more important categorically than other things. The OP suggested that his children have grown up in an area where they're exposed to mixed races. Guess what? They probably genuinely don't feel any different toward their friends who "aren't like them." I'd bet money that if, on the other hand, you were to place an older child in with them (or a young one), they'd probably discriminate far more!
I think the study is flawed. The language used intentionally creates a bias. I think it would have been more appropriate if they had performed a test based upon showing pictures of people of mixed race and then asked the appropriate questions. I'd wager that someone smiling (regardless of color) would probably receive a "yes" if asked if they were friendly or nice. Likewise, someone with a miserable expression would be more apt to be viewed as "mean."
There's a whole lot more to the thought processes of a child than race, I'm afraid. Articles like this do nothing to aid race relations. Counter to the claims, I think these individuals are doing a gross disservice to our society. I guess I'm disgusted that they'd presume children are easily understood and, because of their limited experience, aren't smart enough to know what they're doing by being so judgmental.
Kids are a lot smarter than we give them credit for.