Yeah, that way certain ships cannot have endless area point defense spam, in particular. Maybe the Shattercell is an exception.
Makes sense. The Shattercell is kind of like the upgraded and more OP expensive version of the Machine Gun. The magazine feature in general is something I'll probably look into tonight.
I did start to see a few, but even at the HQ some detachments had no capitals. That said, the Apogee is actually a competent cruiser now, which I'm happy about because I like exploration, and your Squall/3xAtropos build is quite good.
It is possible that the lack of an Orbital Works + nanoforge affects the fleet size/num of capitals despite having High Command. Sci-Corps HQ only has Heavy Industry. You could also be seeing patrols from Lexicus near the station as part of their patrol route. I don't want to just arbitrarily give them an Orbital Works + forge because it effects the sector economy, but you could try and adjust the doctrine settings in the faction file to see if a larger value for shipSize makes a difference.
Also, if you want to test an Orbital Works instead of Heavy Industry you can do so be going to the econ settings under data/config/ArcheanOrderEcon/systems. You will see spreadsheets for most if not all core systems. In the spreadsheet there is a a column to remove and a column to add industries as well as planetary conditions and stations. You can add a row for Sci-Corps HQ and make any changes you want then start a new game.
You'll have to know the ids for these, but for what you would use for this change:
entity id: scicorps_headquarters
removed industries: heavyindustry
added industries: orbitalworks
The code that manages this doesn't currently accept the addition of special items, but I'll probably do that eventually. If you make these changes just remember you made them.

They are there for players to customize non-random core games. At some point they may not even require a new game to take effect, but I haven't coded the logic for that yet since it requires building maps for most of the mod ids and that's time consuming.
WRT Missile ranges:
I noticed there is a Large Salamander now (or has it always been there?) @2,400, so I suppose that I'd only advocate for bumping Squall up to 1,800. I've never thought of it as a DPS weapon. I'd agree with Albreo that either the EMP damage or speed might need a slight reduction. I probably wouldn't do both, at least to start. The only ships that it really does a lot of damage to would be frigates, and the missile don't turn tight enough to connect with them.
The large Salamander has always been there, but I'm sure it is often overlooked for a large missile slot considering other options that exist. I put the Squall range at 1800 for now. I'm thinking about the speed reduction. It is very reliable but its requirement to swirl around a ship means the tipping point to unreliability is incredibly thin and I'd rather it be too reliable over unreliable considering the tier and rarity of the weapon.
I'd agree with the analysis of the Sabot, but it does give me an idea: Are there any fighters left with active flares? Maybe if there were fast heavy fighters and/or maybe a light gunship that specialized in flare spam. They wouldn't do a lot of damage on their own, but would open the door for other strike craft / missiles. Sort of a Wild Weasel role.
Currently only the Claw, Hercules and Krakken have flares and that's mostly just to balance those particular designs to be more attractive when comparing them against shielded strike craft. A Wild Weasel sort of role is interesting though. Maybe a midline fighter armed with a single Micro Repeater or something could work. Once upon a time several other wings had flares, but I find that they are too strong to add to wings that also cause a decent amount of damage.
It's one of the new changes. It's definitely something that you'll want 1 of in your fleets now. Although, I'm skeptical you'll find it worth fielding at 28 DP. Its DPS profile is modestly worse than the 22 DP Revenant (fewer hardpoints/worse fields of fire/worse net dissipation/worse shield efficiency), and much worse than the Legion or Onslaught. Its cost probably needs to fall or it needs a full conversion to Battlecarrier.
Making the Odyssey more of a speedy light battlecarrier is an option. Maybe add a bay or two and increase max OP? It already has carrier-grade bays. Fields of fire is something I will look at as fixing that is relatively easy to correct. I'd rather balance it up to its cost then reduce the cost just in general. That being said, it will probably continue to be slightly worse than a Legion or an Onslaught since it has utility on top of its combat performance.
Also, should the Renegade fighter-bomber count as a fighter for the purposes of the new hull mods? Currently, I don't find them to be worthwhile, but if I could field them cheaply on the Ody or Revenant, I might.
Afaik I think it would change the way the AI uses them if I do that. I'll have to ask to be sure. If so, the biggest downside is they would use their Ion Torpedoes on passing strike craft if I make them a fighter instead of a bomber. I'll see if I can get that to work. Otherwise I'll probably just buff their torpedo a bit or give them more of them, etc.
When your building these variants, do you test them with the pilot personalities that the faction favors?
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Anyway for any faction that defaults to cautious pilots, it's probably worth looking at the variants carefully to make sure that there are enough M/L weapons near the max engagement range of the variant. Otherwise, the addition of a pilot risks making the ship perform worse instead of better.
I don't typically no - though I probably should. I did change and update the Apogee variants from your suggestions. I'll try and keep that in mind as I go through variants.