The only reason amphetamines were ever banned in baseball is because they were scheduled illegal in 1969. The only reason ephedrine was banned is because it was scheduled illegal by the Feds in 2004. Even after Steve Bechler's death in 03, ephedrine was not banned in the majors.
I can take caffeine pills that have the same effect as both drugs. If baseball considered amphetamines a PED, caffeine would be outlawed as well.