For dissipator and capacity yeah its a net difference(but extra OP can compensate), but armor and hull most of the time doesnt matter if your not using it as a battering ram that you should not use it for(its more of a battle barge...
Armor and hull matter a ton for a ship with 30 speed and 1.0 shield efficiency. It has virtually no ability to run or survive if anything ever goes wrong (and things are almost guaranteed to go wrong). If you are piloting yourself, maybe you can play safe, but the AI absolutely needs armor and hull to not die, plus it's a total waste of skills to pilot it yourself. If I am losing the ship in combat regularly and having deal with extra d-mods, that makes it much worse.
If you compare Atlas MK 2 to 40DP capital of course its supposed to lose look at the lasher its also a good/decent ship for its size because its the lowest DP for its class.
If you compare to the Dominator don't forget the AAF and different Mount (2large missile change a lot) , also with militarised and Assault package the difference between those two get a lot lower.
For me what make the Atlas mk2 great is that its cheap in DP and bring the fire power of 2 cruiser for the price of one with more range. its brittle it slow down your fleet but it can punch down very hard and up dencently for 24DP
For like the 3rd time,
I'm not comparing it to real capital ships. I'm comparing it to the dominator, saying that it's comparable, maybe slightly worse at what I would use the dominator for and maybe slightly better at things I don't think matter much, and then saying I don't think the dominator is worth using usually, so by extension the atlas is also not worth using. That's my reasoning, it has nothing to do with comparisons to capital ships.
For what it's worth, I would rather have a real capital ship (Paragon, legion XIV, conquest, odyssey) than two atlases, but that's a much more complicated comparison and I'd rather stick to the simple slow heavy cruiser comparison.
If I wanted to spend ~25 DP on a slow heavy cruiser, I would use the champion which is significantly better than either altas or dominator IMO. But by late game, I would just not use slow cruisers because they aren't tanky enough to fight radiants and other endgame enemies, and they aren't fast enough to escape. In the early-mid game, I think atlas is bad because of campaign stats (fuel/supply cost, low burn etc.). In the late game, I think it is bad because of a lack of survivability, so there is no time when I want to use it.
Also, I didn't consider Assault package, but it costs 15 OP, and gives 10% hull (~6-7 OP), 5% armor (3 OP), and 10% capacity (4 OP), so it's basically neutral in the OP comparison, maybe even slightly negative. It certainly does not close the gap in any meaningful way. I still see a ship that needs to spend 100+ OP to have comparable base stats to the dominator. If you are willing to pay extra fuel and reduce your burn to use the ship, then you are paying the price in a different way, but at the end of the day those are still significant disadvantages compared to dominator that I am not going to just ignore. They matter a lot in the early-mid game.