You CAN have a remnant flagship but the work around is a pain in the backside
Make sure you have said ship in fleet and save game and quit
Go into the ships data file, example radiant
remove the automated built in hull mod, you'll likely need to potentially swap it with something else, like advancedcore
reload game
Now remnant ships can have human officers, yourself included in said ship but AI cores no longer
If you aquire a second radiant, simply reverse said process, your original flagship witll remain under the control of said officer until you move him outof the officers chair, so to speak
This could also mean that you could AI human ships, like a paragon.....
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