Make your ship .entity, .mesh, sound files, strings etc
Add your ship to playerPirate.entity as stated above
Open up GalaxyScenarioDef
Add a "planetItemType": designName "AnyItemNameYouWant" (doesn't show up ingame)
entityDefName "name of Capship .entity file"
"Template:PirateBase" add 1 "YourCapshipItemName" planetItem to the list
Increase item counts as always
All Pirate Bases now spawn with 1 level 1 capship. (for more, add another planetItem to the Template)
You can also make a new template and apply it to individual planets in Galaxy Forge so only certain Pirate Bases spawn your capship.