ART 450 addreses transformer protection and Art 240 addresses conductor protection. Both must be taken into consideration when installing ab transformer. Normally you would select your transformer protection from Art 450 (Primary only or Primary and Secondary) and then select your conductor and overcurrent based on that decision.
In the case of a "Y" secondary or a 3ph 4w secondary, Art 240 prescribes that the transformer primary protection can not be used to protect the secondary conductors so secondary protection is required*. In addition Art 408.36 requires panelboards to have overcurrent protection.
(*240.4(F) prescribes that under certain conditions in a two-wire to two-wire or delta-delta transformer arrangement, the secondary conductors may be protected by the primary OCP device but that does not relieve the 408.36 responsibility for a main.)