I don't understand the experiment: even if there are only two orientation for the spin, the atom, itself, can be in any orientation?
It is comparable to the polarization of light. You can filter it in a certain direction, but it, too, is a quantum property. While light cannot pass through two 90deg rotated polarization filters. Ir can pass if you put a 45deg polarization filter between them. That can not be explained classically.
I'm sure the issues are with the details of how the experiment is explained, but I still don't understand.
Despite that, a magnet acts on it exactly the same as if it were a spinning piece of charged metal. So it doesn't start as a spatial difference, but it becomes one once you pass it through the field.
And one of the ways you can tell it's not the same as a spinning piece of metal is that the amount of spin is always exactly the same, regardless of how you orient the field. It's always that number I gave you above, called h-bar. The only question is whether it's positive or negative; it's going to be exactly one or the other.
That's not what would happen to a regular object. For a regular object, you'd sometimes get 100% of h-bar, and sometimes 50%, and sometimes 0%, and sometimes -100%, depending on the angle between the spin and your apparatus. Just like if you were trying to measure the width of a piece of wood with a ruler: it depends on how you angle the ruler. Somehow, for quantum things, it's always exactly 100% or -100%.
100% things go one direction; -100% things go the other direction. You get exactly two lines, separated physically in space, even though there was no such separation in the original charged particle.