He has no idea what he signed. The executive order does not criminalize flag burning. It directs the justice department to charge anyone violating unrelated laws if that violation involves burning a flag. For example, there are laws banning open burning in many jurisdictions, so if you happen to be on federal land in a space where open burning is prohibited, he has told her justice department to prioritize violations of the open burn law if what you b are burning is the flag. But if you move a few feet over and burn it in a campsite with a designated barbecue pit, you're good to go.
It is like the marijuana laws. Marijuana is illegal in every state, because federal law prohibits it, and supercedes state law. But every administration has turned a blind eye to it recently by declining to prosecute (since they can't possibly prosecute everything).
So just to complete the hypothetical - if you use an American flag to light your joint, expect to be prosecuted for smoking marijuana since you burned a flag to light it.