As per my understanding it's because he want to stay focused on his study and dressing up as a girl grab less attention than being a cute boy. I feels like we would be seeing flashback when he simply dress up like a boy, maybe got bullied or something.
Thats the thing. It doesnt seem like that justifies anything.
He makes a cute boy and a cute girl.
If he dress as a boy, girls will want to confess and boys will bully him because of envy.
If he dress as a girl, boys will want to confess and girls will bully him because of envy.
So yeah, different paths, same shitty result.
If he really wanted not to get bothered by others maybe he should use thick glasses and dress poorly so he looks ugly and people stop paying him attention.