My kid was told to tuck in his shirt during the run of play in a soccer game this weekend, and he did so, as people chuckled. He didn't get a red card, and wasn't banished from the tournament, for failing to wear his uniform as the manufacturer intended.
I officiate soccer, and I do ask that the players tuck their shirts in. The reason why? They are always complaining that someone is grabbing their shirts. If the shirt is tucked in, it's easier to determine if someone is tugging on it. I also told some kid to pull his shorts up because he had them so far down that most of his underwear was showing. The underwear isn't part of the uniform, so I don't want to see it.
I think the reason we get all bent out of shape on the uniform rule in track/xc is because we such bigger issues to deal with. For example, look at the West Region of the DII XC championships. Should officials be more concerned with making sure the lead bicyclist knows which way to go or checking to see if someone's shorts are rolled up?
I don't have a problem with the rules, but there needs to some room for referee discretion.