The traditional HN way is to make up some "It's Just That They Hate Us"[0] teenage conspiracy. The reality is this: amphetamine was widely used medically for decades by the time the Controlled Substances Act was passed. When these acts are passed, governments are usually under pressure to not remove access to things that people commonly use. Therefore, it was scheduled in a category that recognized medical use. This allowed the subsequent development of associated clinical trials and so on. It is much harder to work with Schedule I drugs than Schedule II drugs. So an accident of historical timing is what caused the difference.
0: This game is really tiresome. It's "capitalism". "They just don't want to lose power". "There's no money in it". Thought-terminating cliches. LLM-grade.