This may be a dumb question...

5 volts is the main logic voltage that any board uses. This is adjustable because this can be a little finicky across boards and you get longer life out of the power supply this way since you can adjust over time. It's the only adjustable voltage because most anything else (JAMMA-wise) uses 12 and -5 for audio amps and those aren't very sensitive to being high or low.
 
Amplifying what Pinball Wizard said...different games draw different amounts of current from the +5v supply. It's usually the heaviest draw, but also the largest variation, so the variation of the average value (as a percent of 5V) can be larger from game to game. The other voltages are set up as multiples of the +5v supply and the current draw is usually less which makes them easier to regulate. So they should stay close to their respective targets once the +5v is dialed in.
 
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