Test tones are recorded at different reference levels. Some people prefer to use tones that are recorded at a much higher level than what music is recorded at. This makes sure that no their amps will NEVER see enough input voltage to have a reason to clip. The tone that will cause your HU to clip is of a highe volume than any music. The disadvantage to this is that you'll rarely see anything close to full performance out of your gear. If you can't clip on event the highest peaks of any music, you wont' get much power out of your amp on the more reserved parts of the music either. For music with very low record volumes, this can actually be fairly frustrating, having to crank the hu up to get decent volume.
I usually set gains by ear, but if I had to use tones I'd do a -10db tone at 3/4 hu volume. This will allow put you out of the range of clipping at 3/4 volume for all but the most intense of basslines. If the song isn't that dynamic, you have quite a bit of your volume knob to use as well. The only issue with this, is inexperienced users can often crank it too high on the wrong tracks, and break their equipment.
Think of it as a govenor on a sports car. Some people need them or else they'd die a semi-painless death by crashing into a tree, other's are a bit more conservative. They appreciate the extra power, but don't always use it.