I don't know if anyone's mentioned this already, but the pirate flagship descriptions seems to suggest they're unique (like other IBB ships), but it seems they can appear on multiple occasions in randomly generated fleets, and even be mass produced via blueprints. I suspect this is a bug as other mods' unique bounty flagships don't exhibit this ability to be mass produced or appear repeatedly, but you could have done this intentionally for all I know.
Also, for balance feedback: Deployment points needs a looking at, in my opinion, especially for hybrid transport-warship classes. As someone with over 100 active mods, JYD (and CFT, your other mod) have by a significant margin the highest firepower-to-deployment-cost ratio. In my games I end up using JYD and CFT
transports as my mainline warships due to the fact I can deploy 200-400% more vessels than enemy warship fleets without a proportional reduction in ship fighting ability.
The main reason seems to be because these ships have deployment costs roughly the same as unarmed civilian ships of the same class, but possess the firepower and ordnance of medium-quality warships, along with the corresponding number of mounts with great coverage (most non-front ones usually have 180-360 degree firing arcs). That alone would make them worthwhile, but they also have the additional perk of often have literally the largest cargo bays of their class (or at least top 5) -- again, that's with 100 active mods -- so completely obsolete the need for conventional civilian supply ships and their corresponding costs, fleet size, and enemy detection penalties. Finally since the game classifies them as non-combat ships, their presence in your fleet does not contribute to combat ship fleet composition, so they do not reduce XP gain or scare off enemy fleets like normal combat ships.
Some examples of what I mean:
- Troublesome. Destroyer. Costs 5 deployment points. Deployment cost of a cheap war frigate, but the firepower of a very heavy destroyer or very light cruiser. Also acts as marine support on top of those bonuses.
- Carrack. Cruiser. Costs 10 deployment points, roughly a higher quality destroyer. Its five medium, five small mounts puts its firepower well above destroyers of the same cost. Oh, also literally the single largest (cruiser-class) cargo hold I've seen across the ~40 mods I have installed, with cargo shielding and salvage facilities to boot.
- Intelligent. Destroyer. Costs 5 deployment points. Unlike the others its cost roughly matches its fighting ability (cost of a mid-tier frigate, firepower just below that). But it's noteworthy here because it simultaneously fills almost every non-combat niche at once: it has more cargo than a buffalo (possibly the largest destroyer cargobay among my 100 mods), and in-built hullmods for salvaging, surveying, and boosting fleet detection range. So having these in your fleet can obsolete basically every form of destroyer-tier support ship in existence, except marine support. Which can mean room for a lot more warship in your fleet. That said you can still throw them into battle and they will fight with near parity against other ships of the same deployment costs; they don't suffer for this super-utility by being defenseless ships.