Hi
I believe with the new system you must collect your baggage still if you are connecting to a domestic flight. The bags are scanned behind the scenes but they are all still placed on the bet for connection. The only difference is that since all bags are scanned before coming to the baggage claim, you no longer have random searches in the customs checkpoint after picking up your bags. I have connected at terminal 2 at MEX frequently and this has always been the case.

Also, what was the $50 fine for? Was it taxes for importing merchandise in excess of your allowance or was it for not bringing your baggage through customs?