There is NO bench fee for Guitar Repair. Rates on instrument repair are usually discussed and defined before the work has been done so you'll have an idea of what you're getting into.
There is a $40 bench fee for Amplifier Repair. Since issues with amplifiers are not always immediately apparent and can be very complicated, the bench fee is to cover the techs' time to figure out what's wrong. The good news is that the bench fee is applied to the repair, not in addition to the repair. The bench fee is due when you drop off your instrument.