because 25 atlas are better than 25 hounds. The Atlas aren't supposed to be useful for someone concerned with fuel/cargo efficiency, if you're dividing those two numbers it's not the ship for you
It has damn good stats in vanilla. It's the smaller freighters from mods what breaks it.
And if I was to accept the ship limit being a thing for everyone and affecting shipbuilding industry, what happened then so that no more than 25 ships can travel together, ever?
And let's try to deduce some further lore from UI and gameplay limitations in the current build:
-Like ships, there cannot be too many captains in a single fleet, it's below half the max number of ships actually. Not every ship can a afford a captain these days, you know? Maybe they are all horrible people and bicker constantly if kept in greater concentrations.
-Captains cannot plot automatic course that is not straight, nor can they task another crew member with piloting while they drink their hot Earl Grey. You cannot really trust anyone but yourself. Luckily sleep has been eliminated so that an admiral can personally babysit his fleet 24/7.
-People no longer eat food nor require payment beyond the initial hire. Having a known name and face means you cannot die at all, just like ship captains and station officers. Keeping in contact has become difficult though, you will never meet again a captain you dismissed.
-Planetary conquest is completely forbidden (almost forgot this one thanks to Nexerelin). Despite all the war and misery, people are decent enough that they don't conquer each other's planets or stations anymore. War is waged exclusively to cause annoyance, create trading opportunities and gain experience points.
Wow, the Collapse must really have been something!
You see, I happily overlook gameplay mechanics that don't have an in-universe explanation, unless the world and the way it works is also heavily affected by them. Everything I listed above is silly, but I don't have to be bothered by it. I wouldn't treat my crew different if they died of old age over time. If one of my captains died, I'd probably reload anyway. They are limitations built
around the gameplay so that I don't bump into them while weighing my options.
With vanilla cargo efficiency, the need for cost effective cargo space doesn't drive you into the fleet size limit. You don't balance your fleet against, but within the limit. You want the Atlas because it takes only one slot AND has reasonable costs.
With mod freighters you basically pay fuel and supplies for free slots. You get Eschaton to have it take up only 1 slot INSTEAD of reasonable costs.
tl;dr:
If you base a limitation entirely around gameplay balance or scope and disregard in-universe logic, don't make the player work their way around it all the time. It will only make its artificiality more apparent.