When you have a conductive material (such as a metal raceway) in the presence of a varying magnetic field (such as one generated by an AC current), a current will be induced in that conductive material. That is the basic principle behind a transformer. So if you put only the A phase in a metal conduit, it will cause a current to flow in the conduit. If you put two or more phase A conductors (and no other phases) in a metal conduit, it will induce a higher current in the conduit. That conduit will experience I^2R heating in the same way that a wire does. Current flow causes heating.
But if you put an A, a B, and a C in the same conduit, their magnetic fields tend to cancel each other out. Therefore, there is no (or very little) magnetic field seen by the conduit, and no (or very little) current induced in the conduit.
That is the reason for 300.3(B).