Thanks to everyone for the replies!
It does seem that the Yamaha's pickups are hot, and that the B3 input is too sensitive, and not adjustable. I even tried setting the B3 to active, and I still get the same full-on tone. Even the headphone output from the B3 into headphones is too hot, so it's not the PA mixer causing the problem.
The only amp I have is a Fender Rumble 100, and although the tone isn't so full-on as through the B3, I don't like the overall tone, which I characterize as 'cardboard'. Also, our rehearsals and practices have to be 'silent', so it's IEMs or headphones. Perhaps I need a higher-quality preamp.
Do you DI, or mic a cab?