I think I can explain that pretty easily, at least from my own perspective. I thought of the standard starship components as adding up to mid to long range/endurance, mixed use starships. That saucer is there to house lots of people that almost always include a contingent of researchers doing on-site work. But there would be another type of ship- a warship- that would have very different priorities and have a very small crew. Its range and endurance would be short-medium. No saucer. Just raw shields, speed and weaponry, in differing proportions as the design demands.
So, when you see the FJ dreadnought, I'm thinking "this is as good as we can get for projecting power over long distances within a mixed-use starship hull". For the Federation and Starfleet, getting all those researchers way out on the frontier to figure out what really is out there (and might eventually develop into a threat or opportunity) must be as important as having no nonsense, fail safe weaponry closer to home.