My rationalization for the ship is pretty simple. I've never seen a good technical reason why it couldn't be done. I know, probably the same reason every ship like this exists. Still, we see a ship like the GCS, a combination of science ship, floating hotel, long distance traveler, and speed demon face down dedicated warships all the time and win. So I asked the question, what happens if you take a ship like that, rip out everything that doesn't go PEWPEW or prevent you from getting blown up? Well, we've seen the Defiant, a positively tiny warship with more firepower than a Galaxy but less than a 1/10th a Galaxy's size. Well what if you gave a Galaxy sized ship the same treatment?
It doesn't fit in with the established world very well, I know that. Mostly it just brings some uncomfortable questions to the fore like, "Well why didn't they do something like this before?" Well in this alternate universe the Federation finally decided after the Dominion War that enough was enough and decided to go all out. Far as I can see there's no overriding technical reason the Federation couldn't do it. All the arguments boil down to "Well they just don't do it like this," and I can't argue with that. Which is why this is an AU that branches off of traditional Trek's time line in 2379.
If people don't like the ship itself I'm fine with that. I knew when I started a lot of people would hate it. I don't think it detracts too much from the story itself too much.