Is the ball going to get trapped behind that target flipper at all? And which game did those wireforms come from originally?

Does that 50ms delay apply to the flipper switch input as well? That would be enough to noticably affect aiming.

Would it be possible to do 3D asset-based screen animations in something like Unity, chained to the inputs from the machine driven by the Visual Basic code?

Unity can quite happily do 2D sprites and backgrounds too.