I've seen this kind of thing on other games (maybe Olympics or Rack A Ball?) where the score is what you'd expect but the chime is off by one. I've chased it down once or twice and convinced myself that that is the desired behavior. The only thing I could think of was that the designers were trying to make it harder to predict the match value.
Since the match was often driven by the 00-90 unit you could predict the value of the match number if you could figure out the order in which the match numbers appeared on the stepper contact disc. Once you knew the order you could just remember the last match value and look at the 10s digit to figure out how many steps the 00-90 stepper had taken. Driving the 00-90 unit fewer times than the score reel that would make it much harder to track how many steps the 00-90 unit had taken and therefore what the next match number would be.
That's my theory anyway.
Oddly enough this came up recently on facebook. Someone posted an image of a match predictor that arrived with an issue of the Pinball Trader. Here's mine: