It is arbitrary. While what classification a substance is may have some grounding in research, it's mostly up to what interest group has either lobbied to get something under or whatever group law enforcement wants to be able to get easy charges for. Cannabis was Sched I because it made it easy for law enforcement to get big sentences for minorities and the counter culture participants of the day. Same thing with LSD and psilocybin.
All the DEA scheduling is just pick and choose your charge for whatever ideological ax they want to grind. Hence why things don't line up with reality
Overdose of MDMA can cause seratonin syndrome, which can be fatal; and long term use might be linked to depression and anxiety (again, by the way it interacts with seratonin)
It definitely should be rescheduled too, since it is not dangerous enough and definitely has potential for medical use (couple therapy was it’s original use)