I would go off points. I know it's the boring decision, but then you are guaranteed to still keep the game going if something malfunctions. For example, if the game was Metallica and the goal was Graver Digger Multiball and the grave marker at the end stops registering hits, you have to take that game out of the tournament and everybody who already played will have to play a different game. This way, if the grave stops registering, it's okay because you can grind out points a different way. Plus a points goal allows you to award/penalize progress towards a goal and will minimize ties.

For example... let's say the goal is 10 million.

0 - 1,999,999 +5 penalty strokes
2m - 3,999,999 +4 penalty strokes
4m - 5,999,999 +3 penalty strokes
6m - 7,999,999 +2 penalty strokes
8m - 9,999,999 +1 penalty stroke

Those penalty strokes would be tacked on to the 3 balls they played in their game when they fell short of the goal. So the best you could do on a hole is 1, the worst being 8. It will lead to a lot more variance in scores.

It's also super easy for scorekeeping purposes if you print those penalty stroke ranges and tape it to the backbox.

I ran it in 2015 so rules could have easily changed since then. But from what I'm seeing in the rules, they allow for this exact scoring system.

III. Format Details

1. Qualifying Rounds

Players will complete 2 rounds of 9 Pin-Holes during Qualifying. Each Pin-Hole will consist of a pinball machine with a target score. The number of balls it takes for the player to reach that target score will represent the number of Pin-Strokes earned for that hole. Should a player not reach the target score after a full game is completed, a stroke value will be determined based on how close the player was to the target score at the end of their game.

For example, the target score of CSI may be set at 10 million points. A player will continue playing the game until he reaches 10 million points. If reached, the number of balls it took to reach that score will be recorded for that Pin-Hole. If the player fails to reach the target score after 5 balls are played, they will be awarded a score based on how close they were to that target:

8,000,000 – 9,999,990 points = 6 strokes [80% of par]
6,000,000 – 7,999,990 points = 7 strokes [60% of par]
4,000,000 – 5,999,990 points = 8 strokes [40% of par]
2,000,000 – 3,999,990 points = 9 strokes [20% of par]
0 – 1,999,990 points = 10 strokes [<20% of par]

A maximum of 10 Pin-Strokes per Pin-Hole will be enforced. Scores will be cumulative across all rounds played.