By trade, I am a physicist...
The phase switch on the pre amp is probably because it's a model with a undersaddle peizo and an internal mic. There will a slight difference in the time a particular note is picked up by each of the two "pick up" systems. When you add the two signals up, depending on the phase, or time difference of the 2 signals you can get a big boomy sound or a scratchy trebbly sound, or something in the middle, which is what you want
You can change the phase by physically moving the internal mic or a neat little bit of electronics can do the same thing.
Hope this helps