Sure it'd be hard to make MDMA in any reasonable quantity at home, that's why I reckon the majority of it is made in professional labs, where the right people have been bought off or silenced. There's a stack of money to be made by running amphetamine laboratories, so it's possible that the right people might just "turn a blind eye" when a team of people come in after hours, use the laboratory overnight, pack up and go home in the morning. I don't know much about drug making but I assume it's possible.
It's either that or those nasty columbian drug cartels poach chemists from industry who don't mind putting their skills towards a questionable cause, ie. setting up an amphetamine lab, developing the next super-duper crop of weed, etc etc. (If I was a chemical engineer and someone approached me with an offer of doubling my pay etc etc, I'd say yes!!)
BTW: I think discussing synthesis on here is a bit risque, can you imagine the nightly news if they stumbled on us.. "internet bulletin board used as meeting place for would-be backyard drug chemists" ouch.