So, testing this further, it looks like a good weapon loadout for Atlas2 is dual Squalls, dual Mjolnirs, dual Railguns. Squalls provide long-range anti-shield. Mjolnirs do bulk of the anti-armor and anti-hull. Railgun provides additional damage if an enemy ship gets close into range. A video of this in action can be found here:
https://www.youtube.com/watch?v=oKZrC84jyGUSorry for the quality, I have to video using my phone because my potato running the game is over a decade old and the game becomes even more of a slideshow when it's also trying to record the screen. But it should show the battle clearly enough.
Although the Atlas2 has medium ballistics on the sides, I find that trying to make it into a broadside ship is a bit of a trap. I tried putting HVD on the sides, but what happens is that this makes the Atlas2's advance toward the enemy diagonally, rather than advancing straight toward the enemy, and just turning to expose its broadsides. That's broadside ship AI behavior in Starsector, to approach diagonally. The problem is that the Atlas2 is so slow that this means it advances too slowly toward the enemy fleet, so the additional damage from HVD is canceled out by it being in range less often. So there was no net benefit. Whereas for a ship like the Conquest, it's fast enough that it'll stay in range of the enemy more often even though it's advancing diagonally.
Putting Railguns on the nose however did improve performance, helping it to do some additional damage when it got too close to enemy ships.
The run in the video wasn't particularly good, the Gryphons flubbed on killing some frigates so they spent more time chasing down frigates than usual, reducing the fleet's overall DPS and reducing the concentration of force against the main enemy fleet. I also made my share of mistakes, but it shows that the fleet setup is relatively tolerant of mistakes. This more or less shows how I typically run my tests and how to beat double Ordos: basically, spread my fleet out into a line, kill a bunch of enemy ships quickly during the initial wave, and then parlay that into setting up a U-shaped formation against the incoming ships, so that the incoming ships are met with overwhelming firepower and they can never mount an effective offense and just end up dying. That's the ideal formation that I generally try to get my ships into for these battles. If the enemy fleet breaks out of that and the battle devolves into a bunch of scattered fights, then I know something went wrong, unless I'm doing something like LP Brawlers or something (where a bunch of scattered fights is expected).
Although it might seem like the Atlas2's are overfluxed (970 vent compared with 175 shield upkeep and 1633 weapon flux), in practice their flux rarely got over 50% since they spent a lot of their time moving forward toward the next target rather than firing on ships. So I could probably put less OP into vents and more into capacity to help with them be more survivable.
In the video, the Atlas2's averaged 423 DPS while the Gryphons averaged 427 DPS, so they did about the same amount of damage. However, I've had runs where the Atlas2's averaged about 500 DPS (while the Gryphons continued to do around 425 DPS or so) so the video didn't really show the Atlas2's at their highest potential. (A screenshot of such a run is attached; I took a lot of damage that run just because I had full flux and was gambling that I could vent in time when the final Radiants arrived, and I lost that gamble when they launched multiple Reapers at me in response. Oops. Lost around half of my hull right there.) For example in the video, one of the Atlas2's got rushed by the final Radiants and almost died because I was too far away and didn't burn drive forward enough, so it overloaded and wasn't doing damage for a while. So it comes down properly using the flagship to control the flow of battle, namely making sure the enemy is firing at you the tank instead of at the Atlas2's which are glass cannons.
A note on what I do as the flagship Onslaught: The Needlers are geared for more DPS at closer range. I burn drive into the enemy fleet at lot, drive up their flux, and then use the Proximity Charge Launchers against important targets and to get rid of clumps of enemy ships. Sometimes you'll see me selecting the Hephaestus, but not firing it, so that I can reduce my flux use when my ship is taking care of enemy shields. That helps conserve flux. You'll also see me burn drive and launching the PCL's, which allows me to yeet them farther away than their normal range. It takes a bit of experience but with practice, you can yeet them into ships a bit to either side as well, so those ships get a lot of incoming damage quickly, overloading and often killing them outright. You can see this at 13 minutes into the video (as well as a number of missed volleys during the fight, oops, so I can clearly improve on this technique).
If there is a nearly-dead ship next to an intact ship, then I'll sometimes target the intact ship, so my weapons, which are mostly anti-shield, will start firing on that ship, while my PCL's or Heph (whatever I'm manually controlling) will kill off the nearly-dead ship. This allows me to use the weapons more efficiently, plus if the intact ship's flux is successfully driven up and it lowers its shields, it'll take explosion damage when the nearly-dead ship next to it dies. You can see an example of this at 12 minutes into the video.
Anyway so yeah the Atlas2's can clearly do well as long as they're used with care. They need to be set up in a situation where they can deal a lot of damage at range and not have to worry much about enemy ships getting close, but if so, then they can be a big contributor in battles.