Sort of. The boarding pass you will receive for your first leg lists your initial departure point and your final destination. It is considered your BP for your entire trip. However, you will receive a "re-boarding" pass for each subsequent leg, as you would (I believe) if you were on an actual direct flight with a stop.

An interesting quirk is that once the initial BP is taken, you are credited for flying all the way to your final destination. Back in 2002, I was booked JFK-EZE with a change of gauge in MIA. Weather delayed our departure from JFK, and our onward flight from MIA left without us. We were routed onto the MIA-SCL flight, and I received MP miles for both the entire JFK-EZE trip as well as the MIA-SCL segment.