I guess different airlines have different policies, but where I work the PF calls the shots, including ALL the checklists, regardless of whether it's an Airbus or a Boeing. Obviously the commander has overriding authority if he or she isn't happy. The emphasis is on allowing FO's to run the show (as much as possible) when they're PF to help prepare them for command.
If the commander doesn't have the ability to allow the FO to run with things and recognise when it's necessary to intervene, perhaps he or she shouldn't be there!