Depends on the film, but 2nd unit does indeed shoot with main talent, sometimes entire scenes as well as major set pieces / sequences. I've worked on films where 2nd unit has shot more of the film than main unit, and that includes shooting with A list talent.

I agree it's not "traditional", or the way it used to be, and I doubt an auteur like Malick would work this way, but studio films being what they are with such tight schedules/budgets, it's the nature of film making today – common practice.