Honestly, I’d never heard the idea the Melbourne was the flagship until people started responding to complaints about it in this and WHEtB. I didn’t even see the complaints themselves, that’s how obscure it is. Real tenth-level Star Trek iceburg stuff.
Apparently their evidence is on the
Excelsior that took Hanson and Shelby to Jouret IV. It was unnamed in BoBW, Part I and referred to in the script as a "transport class" -- the model itself either has the registry of the
Hood or
Repulse NCC-25?? (in Preludes, Part I Q&A, it is noted that the U.S.S.
Columbia was the ship to bring Hanson and Shelby to Jouret IV but the scene wasn't shown). And at that point, the
Melbourne's class was unknown. When they did BoBW, Part II, it was a proto-
Nebula class. It wasn't until Emissary when it got changed to an
Excelsior, which was the first ship to be destroyed at Wolf 359 before the
Saratoga. That's their evidence but it wasn't there. And Hanson gives no indication the ship he came aboard was the
Melbourne anyway. The distant-like talk of the ship by Hanson and Picard indicates to me personally it wasn't at or near Journet IV. It was really only the VOY comic Ghosts that says it was flagship but since it was destroyed right away, I highly doubt it.
I think fanon has become twisted. The vitriol for this apparent "travesty" is appalling.