There's a lot of good stuff here! Couple of comments:
1. Defensive Targeting Array making bombers hang out in front of your ship is actually a good thing
if your ship has a lot of weaponry to provide cover, i.e. battlecarriers such as the Legion. It adds roughly 700 su range to their engagement distance; against the Practice Target in sim, Tridents and Daggers will attack it at around 1100 su without DTA (so, 1100 su will attack, but 1200 su will not), and at around 1800 su with DTA. Due to the Practice Target's size, this is roughly equivalent to 500 base range weapons versus 900 base range weapons (assuming GI and BM and ITU) for something like the Legion. It's a big range upgrade if you're letting your fighters stay in regroup mode to take advantage of the replacement rate, and it helps range match the fighters to your other weapons. Plus (the biggest thing for your flagship), it means one less thing for the player to worry about during combat.
2. Related to the above, for example, when testing with the Legion as my flagship, the Legion has 4 Light Needlers and 5 Heavy Autocannons with Ballistic Rangefinder (making them all 900 base range). So the fighters are basically protected by 1671 kinetic DPS (before bonuses are considered) at 900 * 1.85 = 1665 range from the Legion. Other than something like Tachyon Radiants, ships that go after them are going to get fluxed out quick (as with any ships that enter my weapon range in general), so in practice I haven't found them dying/overloading to be much of a concern. The replacement rate stays pretty high throughout the fight.
3. I did some testing on how often the bombers will fire their payload, by moving to 1000 su of the Practice Target (ensuring that they're close enough to not hesitate from being too far away), with DTA, and then counting how many shots they fired (per projectile for Longbow and Khopesh), using light mortar (firing once per second) as a timer. From there, knowing how much damage their payload does, I calculated the theoretical max DPS that they can do assuming all shots hit and they're always firing, i.e. no fighter deaths/overloads etc. The fighters were on the Legion, either in both slots 1 and 4 or in both 2 and 3. The data was:
Wing Shots Seconds Sho/Min Dam/Sho DPSeach
Trident 67 65 61.8 1000 515
Dagger 57 65 52.6 1000 438
Cobra 19 89 12.8 4000 427
Longbow 195 89 131.5 200 219
Perdit 40 68 35.3 1500 441
Khopesh 260 68 229.4 200 382
I only did each test once so the values are basically just sort of an estimate. But other than the Longbow (which does kinetic damage), all the others do roughly similar DPS, with the Trident a bit higher and the Khopesh a bit lower. Note this is the max possible, not actual, since it assumes all shots hit and there are no fighter deaths/overloads etc, but it relates their max theoretical DPS as if they were regular ballistic etc. weapons.
4. So it comes down to how often they hit, and how often they're active (i.e. not dead/overloaded). For the former, to me the big winners here are Trident and Dagger since their payloads will track the target so their hit rate is much higher. (A side benefit is that they won't hit friendlies.) While the Khopesh does have longer range (and this is easy to verify in sim), I'm not convinced that the longer range is worth the increased misses plus the lower hit strength. Also, in DTA the fighters (far as I can tell) don't really go in waves, but is just whenever each individual fighter is close enough that it feels like launching its payload, so it loses some of its ability to provide cover against PD since they're not going to be in sync.
5. Testing Trident vs Dagger on a flagship Legion against double Ordos, their results vary (sometimes Daggers do more, sometimes Tridents do more), but they generally seem to match the ratio of shots above. So it comes down more to whether or not you have the OP to afford them. It is very much true though that DTA means the Trident's slow top speed when doing attack runs doesn't really have to be factored in, since it'll stay close to the mothership anyway. An example video can be found here:
You can see that in general the replacement rate stays pretty high. It's possible to count up how many Tridents vs Daggers died or overloaded in the video, to compare their survivability, but I haven't done that yet. Toward the end, I changed the fighter mode to "engage"; no idea if that makes them more aggressive and fire their payloads more often or not, but I tend to do it at the end of the battle when I go all-in. You can also see me leading a charge several times with the fighters in tow, so that I burn drive in, drive up the target's flux, and then the fighters follow shortly thereafter with their payloads, such as at 1:25, 5:54, 6:56, and 7:32. Very effective.
In general I usually use Daggers, but this is a case where Tridents seem to do pretty well too. They're more expensive but do seem to do more on average than the Daggers. For the Legion specifically, I'm also debating using one slot for Sparks for PD since its engines are unprotected, so it gets hit by Salamanders fairly frequently. It's really a matter of how much OP I want to dedicate toward protecting engines, even though it eats into my offensive power.
By the way, the video is using Starsector 0.97a-RC10, with a double Ordos fleet that's around 10% bigger than the one I used for testing in 0.96a (844 DP instead of 755 DP). Assuming an initial 45 seconds of dead time for the fleets to get to each other, this means that the finish time of 257 seconds corresponds to around 235 seconds with a fleet of the size of the 0.96a double Ordos test. So a Legion as the flagship for this fleet would also have qualified for the 4 minute mark in the list of fleets I did for 0.96a
here; I don't find the Ordos changes (particularly to elite skills) to have changed their difficulty all that much.
On Legion and Legion XIV, you can significantly improve your DTA bombers performance by placing them on the third and last slot on your refit screen. That is because each slots correspond to each of the gaps present on the legion where the bombers/fighters emerge. The first and second slot correspond to the back left / right gap. The third and forth slot correspond to the front left / right gap. By making the bombers emerge from the front , you can save significant time when they come back for a reload and going back to bombing. As placing them in the back will result in increased travel distance and the need for the bomber to turn around since they always spawn facing to the direction of the gap, for bombers like trident that is slow and hefty this can take some while.
That's a really neat observation! I never considered that the fighter slots on the refit screen correspond to physical locations on the sprite.