Re: The Melbourne dilemma.
It's a shame they didn't just give the Excelsior in Emissary
a different name, rather than confusing matters, as I don't think the Melbourne was even mentioned in that episode. It was just a nod to the fans who might have remembered the ship from BoBW.
Your explanation for the high-numbered Excelsior is fine, so it's the Nebula that poses the problem. Given we've never seen another one with those stubby auxiliary nacelles (apart from the ship on Sisko's desk), I'd assume they were a failure. What if the Nebula-Melbourne was a very early prototype, which was initially intended to be the next USS Melbourne. She was a disaster, left in dock, and her name and number reassigned to this newly refitted (or constructed) Excelsior class ship: a fine, state-of-the-art ship suitable for Riker. Nebula-Melbourne stays in dock, untouched and unloved, until the Borg invasion. She's rushed out, with a skeleton crew, and quickly sliced apart. Her replacement didn't do any better, and William T. Riker was left with a very guilty, if slightly smug, sense of schadenfreude.
If you want to explain Sisko's model, perhaps he was on the team that designed the Nebula in the first place, back in the 2350s? Later he left to join the Saratoga, eventually becoming first officer, only to return to Utopia Planitia to build the Defiant after Wolf 359.