What is so wrong with certain rare Federation starships (Enterprise and Yamato among them) possessing dual NCC registries? (one honorific/historic, the other formal)
Think of it this way: We know that Picard's Enterprise was NCC-1701-D. Maybe it was also NCC-71809, just as the Yamato could be both NCC-1305-E and NCC-71807.
I was thinking the exact same thing. Much like the 1701-A is often thought to have been another number (and name) for its build and subsequently changed. Perhaps the Yamato was honored with a change shortly after entering service.