Configuration does vary a bit with what you're concerned about. I personally feel like the supplies running cost of an Atlas is small enough compared to it's capacity that's I just tend to ignore it as a balancing factor. Militarized subsystems is good for sensors (+75 on a capital logistics ship if you're not running 5 combat capitals already), profile (150 is a non-trivial improvement) and burn speed. If you've taken Salvaging instead of Bulk Transport, it's probably the best choice.
Keep in mind, Militarized subsystems does doubles the minimum crew required, bumping an Atlas or Prometheus from 50 to 100, which when multiplied by crew salary of 10 credits, is a 500 credit a month bump in running costs, although credits don't take up cargo space like supplies. If you're using Makeshift equipment, going from 5 supplies to 7.5 supplies because you added Expanded Cargo holds is actually cheaper (~250 plus 30% tax is still only 325 credits) to run without militarized subsystems. Even going from 10 to 15 is only 500 credits a month if you're typically buying off the black market. Making it break even either way, in term of running costs.
In my combat fleets for example, I stay away from Militarized subsystems, since I don't want my fleet wide combat boosts to be diluted. I often take insulated engine assembly to keep signature reasonable (not good, but reasonable) instead of militarized subsystems. But in a lightweight exploration fleet, it can potentially make a lot of sense improving three useful stats.
Well, I have to disagree with you, OP.
It's a capital ship, which will considerably slow you down (even with burn 20 penalties do still apply to the difficult terrain movement) and put a dent in your supply/fuel economy. Early game you can't really afford it (both the price of a ship and its logistical profile), and you're not limited by the 30 ships cap. Destroyer sized haulers are good enough, while Shepherd is a top tier pick with Converted Fighter Bays+Expanded Cargo Holds combo.
Late game (or past the first few years if you're not a complete newbie) credits become practically worthless, thus there is no reason to pick up anything besides supplies and fuel. If you absolutely love to roam outside the Core with the full 300DP fleet for months and months then yeah, I can totally see the appeal. Otherwise there is absolutely no reason to haul around this slow, vulnerable, fuel guzzling monstrosity.
While I agree capital ships will have more terrain penalties, slowing you down, and the logistics capitals have a max burn speed of 9 without skills, I don't see how it puts a dent in your supply/fuel economy. Can you give an example?
The supply and crew costs of the capital logistic ships are about in line with a combat destroyer, which certainly can be afforded at the beginning of the game. Fuel usage is a bit more than a combat cruiser, but the Atlas comes with 400 fuel capacity, for a 67 light year range, 65% better than a Shepherd. If you only need 150 or 300 cargo, then two Shepherds or a cargo destroyer is enough, but if you're trying to deliver 1,000 supplies and 500 drugs to a pirate base in deficit, the Atlas starts looking pretty efficient to me. Or pulling in the loot from 2-3 orbital habitats on a long exploration run. Those types of opportunities are available from the start of the game. In addition, contact trade missions scale to your cargo capacity. The more you have, the more you make.
Just to put some numbers down, 6 Shepherds with Expanded Cargo hold and Converted fighter bay carry 180 cargo each, and individually cost 4.5 supplies and 1 fuel/ly. Or times 6, 1080 cargo for 27 supplies/month and 6 fuel/light year. They reduce survey costs by 30. Spending a story point or two on the Atlas (as opposed to 6 or 12 for the Shepherds), can add survey capability as well, reducing costs by 40. 10 or 15 supplies for 2600 cargo space and the same fuel costs sounds like a pretty efficient deal to me. And 2600 cargo space is definitely usable inside the core for trading. If we're talking about massed Atlases, like 5 or 10, then that is quite likely overkill with 13,000 to 26,000 cargo space, but 1 Atlas will definitely replace a small fleet of frigate and destroyer logistic ships economically. Still like a pure hound fleet with Bulk transport for smuggling operations though.
Although, I haven't tried finding a contact trade mission with 10 Atlases in tow. I should try that sometime.
