OK, I agree with everything you say, and this is exactly what is happening, but the ball kicks out between your steps 3) and 4) (see below)
The way I think it should work is:
1) The Outhole switch closes which kicks off the Bonus Count (not shown)
2) Eventually the Bonus Unit Zero Position Switch closes which fires the Outhole relay (2nd coil down in the schematic)
3) Once the Outhole relay is active it closes a switch (upper left corner) so that the next time the Score Motor 3A switch closes the Ball Count Unit advances (the coil at the top right)
At this point, once the Outhole relay is active it also closes an Outhole relay switch (D) that pulses the bonus step up coil and ball release coil and the ball gets kicked out
4) When the Ball Count Unit advances after the last ball it should fire the Game Over Trip relay (lower right). This should also happen when the Score Motor 3A switch closes because there's effectively no delay through the Ball Count Unit.
5) When the Game Over Trip relay fires it opens a Normally Closed switch which should cut power along the right side of the schematic to the Outhole relay coil and to the Ball Release coil
6) Soon after all this Score Motor switch 4A closes which normally would fire the Ball Release solenoid (3rd coil down), but since power has been cut (both by the Game Over Trip relay switch and by the Outhole relay switch in the Ball Release circuit) it shouldn't happen.