Are those shorts part of the school uniform - for girls, for anyone?
If they are permitted as uniform then sure, send your son into school in them.
If they're not permitted for anyone then no, you cannot send him in them.
Some children might say something (probably older kids) and I would expect the teacher /staff to deal with that as they would deal with any unpleasant comments - calmly with no drama because these are small children.
Your son could start a trend and all the boys might end up in them OR he might come home and say he doesn't want to wear them and wants the grey school shorts - because he's picked up on the social expectation in school.
School is for secondary socialisation -learning more about the wider world and society - moving beyond your family and personal choices and opinions.
Your child is not a tool for you to manipulate to change/challenge society.