If caning was allowed in today’s schools where girls wear trousers, then exactly the same for a girl as a boy.
if a vast number of boys wore skirts, there would be just the same variation as girls, thin straight skirts, thick pleated skirts/kilts. So skirt up for him as well. If you think it is unfair to carry out a punishment immediately for some and make others wait, for what ever reason, that can easily be rectified by making everyone wait.
But I was really talking of times gone by, then there was not generally such a great call for equality from females, a lot were happy to be treated as a girl, and in the past, girls may have been offended by being expected to be the same as a boy.