What he said.
The tone on most effects will only effect the voicing of the effect not your basic tone as such.
Also on the pre amp and amp emulations as well as the Equakizers there are in fact such a thing as a zero on the EQ, which would be flat.
I dare to say though that if you chose to put on an EQ, pre amp or amp emulation your goal is to change your tone anyway.
Which kind of goes to some degree for all effects.
Putting an effect on your bass will effect the output tone, especially if it is a dirt effect.
Even if you set an analog single pedal dirt unit to flat EQ, it will change the tone of the sum of the output signal when engaged significantly.
Finally most of the effects on the B3 do have a blend knob, which allows you to dial in as much of your original bass sound that you wish in, though at the cost of the amount of output of the effected signal.