As the designated crossdresser of my universe I guess, he sometimes crossdresses at school for comfort from his endless insecurities and his anxiety and stress towards his more feminine traits, and is brought confidence and higher self-esteem when wearing a skirt. A more modest outfit compared to what his pony counterpart tends to wear.
I did make underwear tho under the skirt, not that you can see or or probably will ever see it, but it's there. I mean did you expect him to wear nothing underneath? Perhaps the tight panties squeezing his junk is what makes him more confident. Or the fact that he has to be careful not to expose himself to his classmates. Not that he cares or anything, maybe that just enhances his confidence. :P

I also made sure his feet fit in those shoes too, again you can't see it but trust me they are in there. Actually you could see all of this if you messed with the SVG, but you won't, cowards.