Thankfully, there's some really good precedence to fall back on here: Star Trek TV and movies themselves get scale wrong constantly, or play fast and loose with scale for dramatic effect. It's almost comical on occasion.
For instance, the Enterprise swooping in front of the Defiant in First Contact is a great example. Going by that shot alone, an untrained observer might assume the Enterprise to be the size of a small moon (or an Imperial battlestation) while the Defiant approximates a small European towncar.
Let's not even get into how many decks the Enterprise supposedly had in Final Frontier. You can all thank The Shat for that one.
For STO, playability replaces dramatic effect. This is why the Dominion Dreadnought is the size it is and also one reason why we'll never see the Enterprise-J and other impossibly large ships. Unfortunately, this also means DS9 will never ever look exactly right...
The problem is that a lot of the ship size data is never mention on screen, so they have either guessed the info or taken it from some off screen source, or the fx just randomly changes from episode to episode
the jem'hadar dreadnought for example is meant to be about 2-3 times as large as a galaxy as mentioned in valiant which puts it around 1500 metres. for the final episode the fx team made it even larger than that which is the one shown on the chart. so we fly the smaller version.
Even if no one will truly agree on the ship sizes, there are a lot of universally accepted portrayals. Also, just because the player ships are all roughly made to be out similar sizes, doesn't mean they aren't willing to pull "dramatic" BS all the time. Just look at DS9 and K7.