It is OK to have a primary breaker less than the amps associated with the KVA rating of the transformer at the primary voltage, assuming you aren't fully utilizing all of the kVA of the transformer, and the breaker is sized according to what is required for the load. There is a maximum rating of the primary breaker in order to protect the transformer against overload as discussed in NEC 450.3, but there is no minimum. You could put a 150kVA transformer on a 100A primary breaker at 480V 3-phase, if you only had 100A or less of primary-side load that sizes the breaker.
What is (usually) not OK, is using a primary side breaker to indirectly protect the secondary. In your example, that would be the assumption that your 200A primary breaker protects the secondary at 462A, because 462 = 200*480/208. In this topology, it doesn't comply. This is only allowed in certain topologies that qualify, like delta-delta, and single phase 2-wire on both sides. Topologies that line up currents directly across a pair of windings, with no option to redistribute the amps. Anytime there is a WYE system on either side, or a center-tapped part of the transformer, you need overcurrent protection on both sides.
In any case, both the primary and secondary breakers get sized according to the calculated load, at that corresponding position in the circuit. Think of transformers like gearboxes. Gearboxes trade torque and speed, transformers trade voltage and current. V_pri*I_pri = V_sec*I_sec, if you neglect losses. If you account for losses, it is V_pri*I_pri*efficiency = V_sec*I_sec.