As a Stormcloak-supporting liberal (radical progressive, you might even say), I’ve been shocked and even offended when I’m accused of being a racist or worse, simply because I was moved by the Stormcloak cause and the incredibly nuanced character of Ulfric Stormcloak (arguably the best written character in the game).
First of all, no, I am not accusing individuals of anything. I am merely pointing out the trends in the data.
If anything, the trends vindicate you. Liberal Stormcloaks were far more likely to complain about the racism of their side than conservative Imperials, and even you went on to note that some of the Stormcloaks do have issues with race, so if there were a hypothetical test here, you have definitely passed it.
More than anything, I suspect they fear being accused of racism, and so they side with the Imperials. The fact that the supposedly racist Nords (and we have to keep in mind that only a handful of Nord characters say racist things; many Nords show no evidence of racism whatsoever) are pale-skinned and blond-haired doesn’t exactly help their cause. Any liberal is going to feel a bit hesitant to support Aryan-looking people who are frequently accused of racism!
I had not thought of this when I wrote it, but I suspect what you said here is very true. Cosmopolitanism often appeals to liberals when it means empowering people outside of European culture (e.g., minorities), but when the situation is reversed, cosmopolitanism loses its appeal. Native American reservations may by right or wrong, but they are more definitely not the most cosmopolitan idea, as an example.
Within our own times, fear of accusations is probably also a factor. We see the dire consequences of accusations, with or without good evidence, in media all the time. A paragon of liberalism will be cannibalized by their own side, as soon as somebody thinks they said something racist/sexist/whatever. Perhaps choosing the Stormcloaks would be something that could get them an accusation, so they avoid it.