if u join ur own fleets in battle u should be able to ASSUMING DIRECT CONTROL your faction's ships.
i say this 100% bc i want to be able to set my faction to priotize a-kites and nothing else, set the only variant for the kite to be a torp bomber with EMR, then pilot a high tech close support capital ship into battle then when i join my faction fleets use their atropos kites with the reckless abandon of someone piloting someone else's ships while being CAS'd by my own flagship until all of the kites are empty and/or dead
edit: and you can make having "cooperative" status with a faction more meaningful & literal by making it unlock the ability to pilot that ally's ships in battle