Belmont isn't as busy as Western but it's also a big time east/west road. That location being designed to serve cars makes sense.
I'd agree with you that a drive thru designed to serve cars in a walkable area of the city (say the McDonalds on Clark and Wrightwood) doesn't make sense, but this does.
I drive by that intersection three times a week getting my kids to sports around there. It's terrible for pedestrians and is a massive intersection. I never, ever see people running or walking around there.
As for why it's a transportation deadzone, it's 1.2 miles from the Blue Line, 1.1 mile from the Brown Line, and 1.8 miles from the Red line.
That intersection is just a heavy, heavy car area of the city and the drive thru makes sense as other uses designed for walking wouldn't work there.