That's the testament to just how much work your flagship puts in(IIRC from one of your recent examples, it did 31% total damage even though it was accompanied by 8 Gryphons)
Well it's both that plus as the flagship, I'm also more or less controlling the flow of the battle; I can go where the battle line needs some more firepower, I can rush in with burn drive to tank if part of my fleet is under attack too much, etc., which enables the fleet to continue to pump out damage instead of having to go on defense (which cuts into their damage output). Generally speaking my flagship Onslaught XIV averages around 1200-1500 DPS, while my flagship SO Medusa with dual Cryoblasters in an SO fleet averages around 800 DPS or so, while my flagship Ziggurat runs at around 2100 DPS. Compared with a Gryphon putting out around 400 DPS and most cruisers putting out less than 300 DPS and yeah, hence I'm not particularly swayed by reports of
player-controlled capitals being able to put out a lot of damage. Not that they're not important, but my perspective is that many player-controlled ships can usually put out several times more damage than the AI controlling the same ship in the first place. I'd like to get some measurements on the Pegasus but I won't be able to play until I get back from a trip, so it may be a while before I can get some hard testing done to put it in perspective with other player-controlled ships. Fortunately, even with the RC9 nerf, I can still just add the original back as a skin for testing.
It also depends on the enemy fleet composition, some "rolls" seem genuinely harder than others; I'm beginning to think that strength of Ordo fleets varies even between individual high danger systems. Perhaps scaled with distance from core worlds?
From my 0.95.1a data, the first 10 or so fleets from a full Nexus are basically "warmup" fleets, and after that, a single Ordos varied from 250 to 386 FP (average 317.5 FP), and from 278 to 487 DP (average 385.8 DP). My understanding is that the total FP is rolled and then the fleet factory "spends" that FP on the various ships or something along those lines, but I don't know the actual algorithm. But yes there is a substantial variation from the smallest fleet to the largest fleet that you can get. When I selected the double Ordos fleet to use for testing, I deliberately chose a set that was about average so that the data wouldn't be biased against a harder-than-usual nor easier-than-usual double Ordos fleet.
You can quickly tell the FP of a fleet by using the "kill" console command to kill a fleet, which tells you its FP. The DP I counted the old-fashioned way, by having a spreadsheet of how many Radiants, Brilliants, etc., each fleet had, along with the number of each type of core.