Will there be a joint team (MLB and MLBPA) to calibrate the contraptions? Will it be done by an outside entity? Will there be negotiatons to determine what exactly is a "strike zone"? Can the umpire over rule the machine? Will a player be able to challenge (file a grievance) a call based on the last calibration of the device .... akin to challenging a radar gun based on weather conditions, the last calibration, etc.? This could be a sticky wicket.
Don't know the answer to most of your questions, but this one is absolutely a yes. During the game the only person on the field that knows what the machine called is the home plate umpire. If the ump feels it blew a call, he can override it at will. Of course, how many times he overrrode it will become part of the game record and I'm assuming used to evaluate the ump.
It's mostly supposed to be used when the machine totally blows a call, for example a ball that bounces in the dirt then skips up to break the plane will be called a strike by the machine even though it's a dead ball. It also can't rule on swinging strikes outside the zone.