This is what causes a lot of noise and wear and tear. I actually researched this and it seems that it was not as stupid of a decision as a lot of people say it is. There is a problem with beveled wheels -- it is called hunting. This is when the car oscillates from side to side. Hunting is unpleasant, also causes wear and tear and noise and creates a danger of derailing.
Hunting becomes more likely if the car is lighter and if it is going high speed. The bart was designed to be lighter than most existing metro systems and to go much faster than existing metro systems in certain corridors. So they wanted to prevent hunting and thus made a portion of the wheel cylindrical.
So it seems that they just made another engineering trade off. And I am sure they had justification. But I do wish that when engineers make these trade offs they take human comfort into account. I does not seem that they gave sound much of a weight when making their trade offs.
I think the solution is to keep the wheels cylindrical but just decouple them. I.e., not to have the right and left wheel connected by an axle. If they are independent they can move at different speeds on the turns and will not cause grinding and noise. And the wheels that are driven may be driven by different electric motors that drive the wheels by the necessary different speeds on turns. This is called vectoring and is already being done for some electric cars.