Yes, it's true, wearing a kilt is not unmanly. I'd like to see the principal of that school telling a group of beefy Scottish rugby fans that wearing kilts somehow affects their manhood.
But I think that that argument is not the right road to go down, especially as trans people. Afterall, if he wanted to wear a skirt to the prom, why would that matter? It shouldn't be anyone else's business what he wears, be it a kilt or a skirt or a pair of trousers.