I have this same damn issue, esp. when i put the car from OFF to ON without starting it. They damn thing buzzes and pressurizes. Passengers are always wondering what the hell that sound is... " Dude you should get your car checked, maybe there is a recall on the brakes? " drives me nuts!
I suspect it is part of the PRE-PRESURIZER ON THE BRAKES, so that when you have an emergency the system is already pressurized, When the RIG has been running for a while the pressure is maintained from the engine vacuum line.
Too many "tool" features on this rig.
To begin with this is what the dealer told me. But then I had a tech look at it and compare it to other 4Runners. My pedal was buzzing/vibrating all over the place every time I braked - to the point that it was an arguably dangerous distraction. Turned out there was something up with the master cylinder (not just the brake booster). It was vibrating/rattling so much that it was sending the vibration through to the brake pedal. I had the master cylinder replaced under warranty and the problem stopped.