I have not tried, but each faction has this field:
factionDoctrine | commanderSkills
It is an array, so if you put a faction file with just this field into your mod, it should merge the entries with all other mods and core.
Maybe putting the skill into that field could work, but I fear there is no way to mark it as mandatory, so factions with too low
factionDoctrine | officerQuality
may end up having another skill instead.
I have tried to track down fleet generation and I got to
FleetFactoryV3#createFleet
. There should (in vanilla) not exist any CreateFleetPlugin (But check that via debugger! I just glossed over it.), so you should be able to create your own and register it in an implementation of ModPlugin#onApplicationLoad . That should do it.
(In your CreateFleetPlugin, you can call
FleetFactoryV3#addCommanderAndOfficers
and modify the resulting admiral.)